I don't think it hurts the 2nd game at all. It's central to the story. It's simply what happened. But it radically changes things going forward in a way they might not want to have to do right away.This strategy is what I was hinting at. It allows them to tell original story while avoiding the controversial decisions that hurt the second game.
Anyway, I liked the 2nd game a lot. I'm not in the controversy camp.