No, Marcus thought he would EVENTUALLY be a threat.
Is there a meaningful difference?
There is.
Marcus assumes he can eliminate Khan when he ceases to be useful or becomes more trouble than he's worth. That isn't a "long term" threat in that regard because it wouldn't actually TAKE very long to solve that problem.
Hell, it didn't even take the Enterprise that long to track down and destroy the Reliant, and even then after Khan had the advantage of sucker-punching them and their inexperienced trainee crew. It took only slightly more time for NX-01 to track down and eliminate Arik Soong's augments in the Borderlands. Thus, if Marcus is assuming that a renegade Khan could be handled by conventional application of firepower, that's actually a pretty safe assumption.
Marcus set up the blackmail scheme from the get-go
Did he? If you go by the IDW comics, it was actually more of a Bourne Identity scheme with Khan having no idea that his crew even existed.
Leaving that aside, though, Khan's behavior is entirely inconsistent with that theory. If Marcus was really using the crew to control him, he would have used the threat of their execution to force Khan to surrender after the London bombing. More to the point, Khan would have no reason to believe Marcus had killed his crew when his supposed plan had been discovered; in fact, he'd have every reason to believe that Marcus was not only keeping them alive but had gone to exceptionally great lengths to HIDE them in order to reassert his control. In that case, Khan's best move would be to try to capture Marcus and beat the information out of him, not kill him in an airstrike.
Khan isn't behaving like someone who's trying to get his "family" back. On the contrary, he's behaving like someone who has been paid an obscene bounty to do someone else's dirty work.
OTOH, the events of the movie suggest that Marcus has already lost control of Khan, and the crew indeed has slipped from his hands.
First of all, it's not at all clear how or when Marcus lost control of Khan. We ASSUME Khan had gone rogue at some point prior to blowing up the Kelvin archive, but the only evidence for that assumption is Marcus' say-so. We also assume Khan was a renegade when he attacked the Daystrom Conference Room, again based entirely on Marcus' version of events. In NEITHER case is Admiral Marcus being entirely truthful about what's really going on, and it remains a strong possibility that Khan was actually acting on Marcus' orders right up until the moment he surrendered to Kirk.
Second of all, the Augments
never slipped from Marcus' hands. He knew exactly where they were the entire time. Much more interestingly, Khan ALSO knew where they were, since he was able to tell Kirk with absolute certainty that his crew were inside of the torpedoes Marcus had given him.
Think about that for a moment: what reason does Khan have to believe Marcus would give Kirk the very same torpedoes he'd loaded his crew into? Is that a logical thing for Khan to assume if he believes that Kirk was sent here to kill him with a torpedo strike?
OR
Is Khan aware of the torpedo's payload because delivering them to Kronos
was part of the plan?
They do not suggest that Marcus would be eager to let go of control by delivering the crew to Khan's current location...
And yet we never SEE Marcus use the augments as a mechanism of control. That, again, is part of Khan's spiel and we already know he's full of it.
The fact is, based on Khan's behavior, it's a lot more likely that the cryo tubes weren't a form of blackmail, but a form of
payment. "You do this job for me, and I'll give you back your people." That would be the creepy hidden meaning behind Khan's performance in the brig: "Is there anything you wouldn't do for your family?" That line doesn't make sense if Khan believes his crew were dead, but it makes perfect sense if agreeing to murder all of Marcus' political rivals is only way he can convince the Admiral to set them all free.
THAT deal fits pretty well with what we already know about Khan's history:
Marcus: Conquering Kronos won't be easy. They're a warrior race, they don't like outsiders. They believe in promotion through the assassination of superior officers, and they don't particularly like aliens. It's going to be very difficult...
Khan: Have you ever read Milton, Admiral?
Marcus: (nodding) Once you blow the archive, you'll only have a few hours to prepare for the strike. Everyone on the list will be in attendance. You better make good, Khan, or so help me I'll fire those torpedoes into the sun.
Either Khan is ineffective in what he does, or he is laying a trail of evidence for others to follow.
Or he doesn't have any particular reason to BE clandestine because he knows the only person who's actually looking for him
is the person he's working for.
Since we see others following him along such a trail
No we don't. NO ONE is following Khan's trail except for the people in the Daystrom Conference Room. That's explicit from the film: Marcus mentioned that "Starfleet has jurisdiction" which means local authorities in London aren't investigating the incident. Starfleet (meaning Marcus) has pulled some strings to keep the civilian authorities from getting involved.
Which means any surveillance footage of the attack -- or any evidence at all that might have lead to Khan's whereabouts -- would be in the possession of Starfleet, and ONLY Starfleet, which will only act on that evidence in a way that Admiral Marcus directs it to.
If Marcus is in on it (which he is) then Khan knows that the only people who are following his trail are disposable patsies (which they are). That means part of the trail -- the coordinates on his beaming device -- can be left deliberately. The rest of the trail is simply irrelevant.
So Marcus wouldn't send Kirk on the scene while knowing about the crew and the way in that it offered to Khan.
That begs the question of why Marcus put the augments on the Enterprise in the first place. If his goal was to eliminate Khan, he would have given him non-modified (stealthy?) torpedoes and then dropped all the cryo tubes into the Great Red Spot.
Failing to tell Kirk about the augments poses a certain tactical risk, and yet there's no actual BENEFIT in loading the augments into the torpedoes that will be used for the assassination (it's actually A LOT riskier than disposing of them separately). Unless, of course, it's not really an assassination, in which case his not telling Kirk about the augments is a practical necessity.
Khan may have been sent to wreak havoc on Qo'noS. But from that it follows that his crew either should have been sent with him, without all this public gesticulation (if Marcus trusted Khan), or that his crew should have been kept carefully under lock and key (if Marcus did not trust Khan).
You're forgetting the "Start a war with the Klingons" angle, which requires a starship to be blown to bits in the neutral zone. A fundamental problem with THAT plan is convincing some poor dumb bastard to fly his ship into the neutral zone and then do something that causes to Klingons to blow up his ship. Marcus probably would have given that dubious honor to one of the ships that had just lots its senior officers in the Daystrom room, but then Kirk volunteered, and seemed to already know that Khan was on Kronos and therefore was already a potential loose end to be disposed of.
More to the point: Marcus DOESN'T trust Khan, and therefore won't give him his payment until he has actually completed his assignment as ordered. Reuniting with his crew is Khan's reward for a job well done, but even then, Marcus doesn't actually WAKE the augments for the reunion and even rigs the torpedoes to explode if anyone tries to open their tubes.
What we do know is that he set up this S31 search for esoteric means of unspecific, long term survival and prospering of the UFP. He wasn't a one-trick pony
Correction: Section 31 isn't a one-trick pony. Admiral Marcus, however, is neither the founder nor even the most prominent specimen of that organization. Quite the contrary, he appears to be a rather unhinged and power-hungry aberration, which is more or less confirmed in the IDW comics.
If the S31 bombing and penthouse massacre wasn't jointly planned by Marcus and Khan, then this would be the Admiral's wake-up call for what Khan can achieve.
Exactly. So why the hell did he leave the augments in those torpedoes?
If, on the other hand, Marcus was in on the plan, then leaving the augments in the torpedoes finally makes sense. Marcus not only knows what kind of havoc the augments are capable of, he's actually COUNTING on it.
Now whose idea would that be...?
Undoubtedly Marcus, although Khan would be made aware of this and briefed on how to safely open the torpedoes without blowing himself up. The point of the booby trap isn't to kill Khan, it's to prevent the Klingons (or anyone else) from finding out what was inside those torpedoes.
Enterprise fires the torpedoes. The torpedoes land at Ketha Province, soft land and are recovered by Khan. While Kirk and crew are scratching their heads wondering how it is that all 72 torpedoes turned out to be duds, the Klingons trace the firing points of the supposedly (but obviously far from) untraceable torpedoes straight back to Enterprise and blow it out of the sky, eliminating anyone who might know how the augments got there in the first place. This way, if the Klingons accuse Starfleet of planting Khan there, they can believably claim ignorance (not that the Klingons will care, but the Federation Council certainly will).
This is a plan that Marcus could order Khan to execute, while always intending to backstab him instead. And it's a plan Khan could suggest for Marcus, in order to arrange for a backstabbing scheme of his own.
However, it's not a plan that I could ever see executed. It is not in the interests of either party, and both must respectively realize that.
That doesn't follow. It's VERY MUCH in the interests of Marcus, who has the opportunity to plant 72 incredibly formidable super-soldiers behind enemy lines with no paper trail and no strings attached.
You could argue that it's not really in the interests of Khan,
but Khan is the only one who knows that. He could easily convince Marcus that a chance to conquer a whole world of their own -- even a world as crappy as Kronos -- is an acceptable compromise, made all the more convincing by the fact that Marcus DOES have the cryo-tubes under lock and key and effectively has Khan by the balls.
We know this scenario is plausible because Khan made a similar deal with Kirk under similar circumstances in "Space Seed." Marcus, who has no firsthand experience with Khan's deviousness, has no reason to believe that marooning them on Ceti-Alpha V would be less dangerous than marooning them on Kronos, and
every reason to believe that sending them to Kronos would be the Empire's worst nightmare.
The only thing Marcus doesn't know (yet) is that Khan is as devious as he is brilliant. Finding out that Khan let himself be taken into custody by the Enterprise was probably his
first clue...
Given that none of the torpedoes detonated while Vengeance was kicking the crap out of the Enterprise, they don't seem easy to detonate otherwise.
OTOH, it appears to be trivially easy to bypass the detonation if one wants to access the innards. After all, that's what Spock and his crew did
No, that's what Carol Marcus did after having studied Section 31's weapon designs for the last several years, and then passed that information on to Doctor McCoy, who passed it on to the engineers. Like most things, it's not actually difficult to do
if you know how.
But then, how many Klingon bomb technicians have spent any amount of time studying classified Starfleet weapons technology?
At the very best, a single torpedo might detonate if tampered with. So why bother? If Marcus intends to kill Khan with such a blast, he'd be much better off removing the crew and using a proper torp!
That's exactly my point. It therefore follows logically that
Marcus never intended to Kill Khan.
And if you think about how the entire situation is framed, you have to wonder why exactly Marcus would have taken the risks he did, trying to combine his "Start a war with the Klingons" maneuver with "dispose of Khan and his crew in the most convoluted way possible" plan. Doing so introduces a whole lot of unnecessary risk into two already high-risk gambits, and Marcus deliberately avoids doing sensible things in order to make those two plans work together.
My theory is that this was all about the Klingons from the very beginning, and even Khan's attack at Daystrom was meant to clear house in preparation for combat (as Marcus says: "If
I'm not in charge, our entire way of life ends!"). The plan only went awry when Khan realized he didn't have to play along with this Klingon bullshit anymore and decided to turn the tables on his handler.