Naruto is probably not the type to hold something against someone for the things they did. As long as the person accepts his mistake and is willing to pay the cost for his mistakes, Naruto forgives him. He'd instead say that "It was due to all this that you did to me, I am able to come this far!" Naruto wasn't affected and influenced by Nagato's death? Well, okay if that's what you want to believe in
I prefer to think it was Naruto who influenced and affected Nagato, not the other way around