My moral dilemmas in STID are:
1. Kirk punching out a prisoner
2. The proposal of killing Khan with 72 missiles
Yes Kirk punching out a prisoner was wrong but really who looked bad - just Kirk. Khan didn't care. Kirk was beneath his contempt. I suppose its meant to show us Kirk was pretty volatile, Khan was a superhuman and how Kirk felt about Pike's death.
I'm going to give you the condensed version of how stupid the 72-missile thing was on everyone's side. Marcus was stupid for putting 72 super-missiles in Kirk's control. And why would Kirk fire all 72 missiles anyway? And where was he going to aim them? And was he going to destroy a section of planet without checking if it was occupied (which it was)? Did Kirk think the Klingons were going to sit by while he stayed on the edge of the neutral zone and lobbed missiles at their planets?
I was thinking it was very wrong for Kirk to even entertain Marcus's proposal. But you know when you're in the military sometimes you have to follow orders from the upper echelons without question because TPTB might be in the know about something. It just happened that Marcus was corrupt. But if he wasn't then Kirk was duty bound to follow through as was his crew including Scott.
PrimeScott would have followed Kirk's order's no matter what unless he considered him insane (Turnabout Intruder). In Taste of Armageddon he was prepared to raze a planet on Kirk's orders. He trusted Kirk to make the right decisions when he was in his right mind.
I had thought that Prime Kirk would never obey a dodgy command order but I considered 'Enterprise Incident' where he and Spock stole the cloaking device from the Romulans. As far as we know this wasn't a desperate act to save the Federation from destruction but something thought of to keep the balance of power. I think in the 60s it was considered justifiable to commit espionage if you were on the side of 'good'. But know it seems to me that Kirk's actions in that episode were morally wrong. Perhaps as morally wrong as the potential deploying of deep range missiles into Klingon Sovereign Territory in STID.
Two things:
First, Kirk apparently came to most of the same conclusions you did, which is why he didn't fire the torpedoes and tried to arrest Khan anyway. Trying to punch him out would be a "nobody's looking, this one's for Pike" moment that backfired hilariously.
Secondly, you're assuming that Admiral Marcus was doing a patently immoral thing by trying to have Khan blown away with 72 torpedoes that (sadistic/ironically) also contained the corpses of his buddies. Have you entertained the possibility that Marcus was actually PLAYING Kirk and that those torpedoes never would have detonated at all, but instead would have simply soft-landed on Qo'nos and Khan and his people would have gone on to conquer Qo'nos and use it as a Section 31 proxy army?
To the second point, considering how little hesitation Marcus showed to destroy the Enterprise and its entire crew just to keep Khan from getting the upper hand, it's possible that Khan was still acting on Marcus' orders when he gunned down most of Starfleet's brass and that Kirk's flash of moral clarity (and Khan's decision to
exploit that morality for a chance to conquer a less shitty world), in which case the "moral" of the story is "Never trust the military."