This is a pretty strong indication that her "assumptions" are, in fact, proven correct. In fact, it is only your assumption that she was relying on assumption, which she did not seem to be. What you have not done is proven your contention that she was proven wrong.
Oh, have no fear, that will follow.
Things tend to be pretty simple in movie drama. Typically, heroes and their sidekicks start out not knowing things while villains know things, and the story enters a dramatic turning point when the heroes find out; usually, this coincides with the audience finding out, although sometimes the audience is told first. ST:ID only complicates this by having two sets of villains.
Here, Kirk and Carol Marcus are under the assumption that torpedoes go boom. That's fair for heroes. Khan is under the assumption that torpedoes will
not go boom, though, and he should know.
a) He built those damn things, and he built them for the purpose of not exploding.
b) When he commands that these torpedoes be beamed onboard his ship,
he never once stops to consider the possibility that they might go boom!
What Admiral Marcus knows is fuzzier, but it's pretty clear what he wants out of the torpedoes. Klingons will not go to war unless those torpedoes go boom!
That's it in a nutshell. Everybody
but the man who built those torps wants a kaboom. And when that man gets the kaboom, he is taken completely by surprise.
Marcus wanted Kirk to shoot the torpedoes, not hand back any hostages.
Which means Marcus would have no motivation to put bodies in the torpedoes if it cost him an ounce of kaboom potential.
For a rare once, a violent Star Trek movie has no element of vengeance into its plot. Marcus wants nothing of Khan; to the Admiral, it's irrelevant whether Khan lives or dies, whether he is hurt or satisfied. Marcus just wants explosive devices to go boom in the Klingon desert, with a crippled starship left bloody-handed in the scene, so that a war could be launched.
To put bodies in those torps would be a case of Rube Goldberg twirling his moustache. It makes no sense logically, and it makes no sense dramatically. Alex Marcus is not a character driven by emotion, he's a character exploiting the emotion of others.
In contrast, putting people in those torps is an eminently logical act for Khan, a man chained to a torpedo lathe. Murdering Starfleet personnel is a logical second step, giving Marcus his excuse for launching the war-starting plan. Because as the result, 72 torpedoes are sent to a location where all Khan has to deal with is a single starship with a captain whose primary qualification for the mission, as per Marcus' plan, is being gullible. Yet Khan would risk everything by leaving warheads in those torps...
The only missing element is the pre-events scene where Khan, still "loyal" to Marcus, convinces him that 72 torps is the perfect arsenal for getting the war going. Or perhaps he says that more would be better, but then takes care that all but the 72 are lost in the explosion.
Yet for some reason, by Picard's time his reputation seems to have changed?
How so? He's not a "war criminal" in any TNG or DS9 or VOY episode, either. He's just an example of the dangers of superhuman improvement - a leader too potent for anybody's good.
You may be misinterpreting Space Seed somewhat. For one thing, a tongue-in-cheek comment about a lack of atrocities during his rule does not mean that he was never guilty of war crimes at any point. This is still a character who was willing to kill the Enterprise crew one by one, not to mention his actions during TWOK.
The way the writers
wanted "Space Seed" to be read is obvious: all the talk about Khan being a benign tyrant is there to prevent the character of Kirk from being dealt a crippling blow. If Khan really were more evil than Kirk thinks, the Captain would be proven a fool for believing differently - and a villain himself when letting the superman go in the end.
It would be a plausible story development for Kirk to be a fool and a villain, but not a dramatically acceptable one. Which is why Khan needs to go from black to pale grey before the episode can be shot.
The rest doesn't really change that. Khan is a ruthless soldier who is good at killing the enemy, but he never kills any of Kirk's crew - and even in his later throes of madness, he "maroons" the crew of the
Reliant rather than slaughtering them!
I am 99% sure that Marcus was playing Kirk and intended for the torpedoes to soft land so that Khan would lead his platoon of augments in a "Bay of Pigs" style invasion of Qonos. Khan betrated Marcus, partially because he's the only person on Earth old enough to remember what a total fiasco Bay of Pigs really was, but also because he doesn't want to rule a toxic shithole of a planet like Qo'nos and figured out he could use Kirk's moral fortitude to have his people delivered to a much more attractive target.
A clever idea as such, but it would require arming the Augments somehow. The torpedoes did not contain personal weaponry... And Khan's sports bag could only hold so much.
Also, this would require Khan's slaughter of Starfleet top brass to have been part of Marcus' original plan - otherwise, the Admiral could not rely on Khan still doing his bidding, and the mission would be aborted. This is a possible interpretation of the events, but probably not the preferable one.
This brings up another question I've had for a while: did no one in Section 31 question why this guy they just hired was redesigning their super-secret torpedoes to include a cryotube?
The fact that the tubes could be removed so swiftly suggests that they could have been inserted just as swiftly. So the "the tubes look like fuel cells" thing, combined with a bit of automation on the assembly line, should take care of that. This, plus everybody down at the assembly floor having a healthy fear of the Admiral's mad dog of an expert.
My assumption is he didn't want Enterprise to actually start a war by doing something as overt as attacking Kronos, but intended for her to be caught and destroyed by the Klingons just futzing around in the general vicinity.
The big problem with that is that the Klingons
did not observe anything! Not even when Kirk spent a lot more time in the area than originally planned. Clearly, the edge of the Neutral Zone is a tactically viable location for safely launching a standoff attack without being noticed - which is a relief, because otherwise Kirk would appear not just a hothead but an airhead as well.
And yes, we really don't know how many torpedo tubes the TOS Enterprise had.
Six is the minimum, as per the reference to "photon torpedoes 2, 4 and 6" in "Journey to Babel". And that's just the forward tubes.
(In theory, it might be possible to fire "torpedoes 2, 4 and 6" from a single tube, but it would sound very odd. This type of numbering is supposed to reflect how things were done back in WWII. Also see "The Changeling" for a numbered torpedo that really has to be a numbered torpedo tube.)
Satellite/probe deployment, surveillance equipment deployment, sensor buoy deployment, mine-sweeping, mine-laying, convoy escort, planetary defense, etc.
...Especially since the tubes supposedly all are directly reached from the main shuttlebay. They appear to be generic deployment chutes rather than something sized exactly for these super-torps. This doesn't mean their purpose wouldn't be purely military. But since the purpose of shuttlecraft is not purely military, and these are just "alternate doors to the shuttlebay", we can certainly speculate on a scientific or logistical emphasis for the holes.
Timo Saloniemi