Sasuke will not let Obito kill Naruto because he will and feels like he has to.
It's like how Vegeta saved Goku sometimes in order to take him out himself later on.
Sasuke saying "Not You..." "*I* will be the one, to delete the past!" IMO might be Sasuke's way of wanting Naruto to finally come to terms with the fact he isn't his friend any more, and no one but him will be the one to beat Naruto.
Ah so apparently he wants to kill Naruto, and he won't allowed Obito to kill Naruto, so Naruto will be killed only by Sasuke's own dead, am I right? Oh my gosh...