I'm starting to worry that TVD is abusing protagonist privilege.

This is an excellent way of putting it. I'm worried about the exact same thing and I think the show tends to lose sight of this sort of thing when it gets too caught up in admittedly entertaining character drama. I like moral ambiguity, but only when it feels like intentional character development and not like the writers just can't be bothered to create real consequences for immoral acts by their "good guys."