Nero murdered 6 billion. Kirk Prime (and Chris Pine's is just as "real") never came up against ANYTHING like that - not from anyone accountable (i.e. not the doomsday machine)
Khan had every intention of killing billions with the genesis device, kirk still did not blow him out of the sky when the reliant was a sitting duck. That is the character of kirk, and the mark of a good starfleet officer who practices the principles espoused by the federation.
He still lead him into a field that disabled his shields and left him to die in an explosion. I think he gave khan another chance just like this kirk did with nero it was refused and khan was ditched there. Very simmilar to 2009 kirk.