I agree that the story is very much about Jon, which is why I doubt that he will be killed off permanently.
GRRM could do it though if he really wanted to. Ok, so Jon is a Targ. That doesn't make him an invincible superhero and the only person (besides Dany) who's capable of defeating the Others and ruling the realm peacefully. And the whole AAR thing could turn out to be nothing more than legend and superstition.
Personally, I think ASoIaF would be a hell of a lot better off without going down the cliche "Chosen One" route.