That's basically the twist. Best save because you did all that shit for them you might as well let them live. Or if your pissed that you had to do that just to save them you could kill them...hmmmmmmm....LOL
i think they should of had a choice to kill or let vaas live like with citra. if you killed him, the game proceeded as usual. but if you let him live, he would come back later and kill citra for you. then be like, "peace out, hermano. im out"