Khan wasn't stupid, and he had a starship crewed by a handful of supermen, coupled with potentially the most powerful weapon/technology in known space. The truth--that it was ONLY a weapon because of the protomatter--would only help him.
I think he could have carved out an empire for himself somewhere, and with Earth wiped out because it lacked humpback whales, then of course the Klingon Empire screwed over after Praxis, he'd be in a nice position to create and hold such an empire. Details? Don't know enough of 'em.