I think Gene's disagreement was more in the story formula. It would have benefitted from being more of a moral dilemma and the Genesis device which should have disgraced Carol Marcus and her son and should have included the Klingons IMO. They could have supplied the protomatter and forced him to use it through blackmail. That would have been more interesting than a moustache twirling villain all the way though. It would have been interesting if Khan redeemed himself at the end too overthrowing the Klingons and their threat to kill whoever.