I think it would have been more in the spirit of Star Trek that Khan stayed in alliance with Kirk and that maybe it was Marcus who compelled Khan to do the killings. And that in the end Khan volunteered his blood to save Kirk. Then they could just let Khan and his crew go in the crippled Vengeance because like Kirk and co maybe Khan learnt a lesson. Well of course they would write it a lot better and less lame than I described. And I'd even probably like Marcus to be less villainous and more pressured by having to defend the Federation from Klingons, Romulans, time-travellers etc. And reluctantly sacrificing Kirk and his crew rather than seeming to take some satisfaction from it.