Yeah so instead of revenge against Salamander Hanzou and Charmander Danzou, he wants to kill everyone? His story is a story that is told a million times in a war torn area, and he essentially became the person he hates, and sows more like him, the question will be, can Naruto break the cycle?
If the answer is no, then Pain must die, however, if the answer is yes, the Naruto must let Pain live, and that is the problem, because he can always attack and destroy ...