Look at it from this perspective. You're Kirk, on the Vengeance with Scotty and Khan, working your way to the bridge. Here's what you know:
1. Khan is a genetically enhance human who effortlessly beat about a platoon's worth of Klingons.
And saved Kirk's life in doing so.
2. Admiral Marcus considers this man and his crew to be a big enough threat that he orchestrates two schemes to get rid of them.
And sabotaged the Enterprise
and almost destroyed Kirk's crew in order to start an unnecessary war that would kill millions if not billions. Why in the hell would Kirk be sympathetic with anything Marcus believed? Sure, he didn't trust Khan, but at that point he had no reason to perceive Khan as a worse threat than Marcus. The only person he had any reason to suspect of planning mass murder was Marcus.
STiD Kirk takes option 1 and we all know where that ended (it probably would've been worse if Spock hadn't rigged that torpedo to detonate).
See, that's the root of your mistake. You're basing your argument on what you
know after the fact, rather than putting yourself in Kirk's head and considering what he
knew, and more importantly what he did not know, at that point in the film. You're saying that Kirk should've perceived Khan as a threat so heinous that killing him was the only recourse, but he could not possibly have known that yet
. He certainly had reason to mistrust Khan's intentions and to keep a close eye on him, but also to consider him a tenuous ally against the greater threat of Marcus. He had absolutely no reason to default to killing Khan at that point. It would have been immoral and probably illegal for him to kill Khan before Khan had posed a clear and present danger that justified escalating to that kind of response. You can't fairly condemn a man for failing to act on information that could not have been available to him yet.