That's a bizarre argument. Kirk had no advance knowledge that Khan intended to do anything of the sort -- because Khan didn't. The kamikaze run was not part of Khan's plan; it was just the only move left to him once the ship was crippled and his plan to recover his people had failed. The Vengeance was already falling toward Earth, and all he could do was try to aim it at his enemies. There's no possible way Kirk could've anticipated something that even Khan had no idea was going to happen.
Indeed, Kirk did know that Khan was potentially a threat and he did make a reasonable effort to restrain Khan by stunning him, but he underestimated Khan's resilience. Spock then beamed him and the others back and used the torpedoes to disable the Vengeance. As far as Kirk knew at that point, the threat was ended, and he had other priorities like keeping his ship from crashing (something that happened partly because of Marcus's sabotage, I believe), something he gave his life to prevent. Even if he had known that Khan still had enough control of the Vengeance to put it on a collision course for San Francisco, he would've had no ability or opportunity to prevent it.
So it's completely nonsensical and factually wrong to blame Kirk for what happened. It was Khan who bears the primary culpability since it was his decision to commit the act; and Marcus bears secondary responsibility for driving Khan to that extreme, giving him the means to do so with the Vengeance, and crippling the Enterprise's ability to counter it.
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.
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.
3. Khan is helping you get to the control center of an extremely powerful warship on purpose
and is probably going to betray you there (Kirk tells Scotty that they're helping Khan, not the other way around in the novel, can't remember if that happens in the film).
4. After storming the bridge, the only people who should be conscious are you (Kirk), Scotty, Khan, Carol Marcus, and maybe Admiral Marcus.
5. Since Carol Marcus and Scotty aren't trained to fight and you have repeatedly lost fights to Vulcans and Romulans when quickly stripped of a gun, Khan will likely kick all of your asses and take over when given the chance.
6. There is no hope for getting backup from the Enterprise; Khan must taken out in an ambush as quickly as possible before he can enact his plan (whatever it is).
7. If you fail, people are probably going to die.
Now, what are your options?*
1. Stun Khan. Should
work, but Bones hasn't had the time to run a really thorough analysis on the guy, so you don't know for sure.
2. Set phaser to kill and shoot Khan. Probably
will work, although you don't know since Bones hasn't done that analysis.
3. Shoot Khan multiple times with kill setting phaser. Almost certainly will
work, unless Khan is so radically different from humans that he should be considered a whole separate species or he is Jesus/random alien religious figure that died and resurrected himself/Tom Paris in Threshold.
4. Any of the above, plus shooting the consoles. The safest
option, but the one least likely to be taken since the Vengeance could be used to tow the Enterprise (which is pretty much dead in space) and be a useful part of Starfleet.
Okay, option 4 is pretty much off the table. Let's run through our check-down list: Option 3 is the most logical/common sense "better safe than sorry" choice, and probably the choice most people would take in that situation. Options 1 and 2 are pretty equal in their chance of success and give Khan the highest probability of achieving his goal.
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). Option 3, even considered in a vacuum with no knowledge of how things eventually turn out, only requires the death of one
person who probably can be only taken down with lethal force anyway (unless you're an enraged Vulcan) and is a known murderer, gets a starship's worth of evidence of Section 31's crimes, and
gets the admiral indirectly responsible for Khan's crimes. Kirk's bad decision making is the only thing that allows Khan to take over the Vengeance, which makes him responsible in part for everything that happened after that.
If I was Starfleet Command, I'd toss him out with a dishonorable discharge and give the Enterprise to Spock, since he's at least competent.
*I was going to put "Give a Kirk speech" here, but then I remembered that Kirk was getting verbally pistol-whipped every few minutes by everyone, so it wouldn't have worked anyway.