Khan would kill his family. It was clear that this father would do anything to save his daughter.
Dramatic license? Perhaps, but I've seen it before. It worked well enough for the story.
Logic and rationality don't always work when talking about saving the life of your child. It's not a matter of knowing Khan's capabilities; it was a matter that his daughter had limited time to live and he felt like he must act. Federation medicine had failed him and he was desperate. He wasn't thinking of what his daughter would think of him-he wanted her to live.
Sigh. Khan and the man who was responsible for those deaths were victims of circumstance, of course he would've altered that mindless decision if he thought the real villain didn't have all of the cards. The interrogation scene wasn't enough to make that point? It's easy to make a reasonable judgement after those kinds of events but not when the psychological gun is pointed at their heads at the time.
Um, yeah. That's kind of the point of the entire movie. That Khan's offer to help is always in Khan's interests not the other party's. Marcus, Kirk, and Harwood (Clark's character) all learned that the hard way.
I've had some issues with STID (mostly to do with the "KHAN!!!" scream but that's an argument for another thread

), but the whole saving his daughter scene was not one of them. Khan saved his daughter's life. Yes, in retrospect someone in Khan's position would probably wait to see if the Section 31 agent carried out his side of the bargain, but then again, the agent probably wanted to know his daughter would live before he sacrificed himself and all his colleagues, so it's sort of a chicken and the egg problem.
Whatever the reasons, I never took issue with the agent carrying out the attack after the fact. My guess is Khan probably just held something over the agents head. Khan's a smart guy, he probably had ways of ensuring the deed was done. He was on the scene in fact, probably to make sure the agent did what he was supposed to. That's really a non-issue to me. Could Abrams have been more clear about why the agent did what he did and not warn his Section 31 superiors? I suppose so. But let's face it, no movie can possibly cover every little angle and plot hole. And in this case it wasn't really critical to the overall story the movie was trying to tell.
And yeah. Marcus is most definitely a villain in the movie, but so is Khan. No one should mistaken Khan for some misunderstood bad guy who just wants justice for his people. That's one trait he shares with his Montalban-version. He's out for himself first and foremost. In fact, Captain Kirk even says that on the
Vengeance when he and Scotty are trying to catch up. Scott says he thought Khan was supposed to be helping them when Kirk quite astutely points out, "I'm pretty sure we're helping
him."