One possible motive could be a deep misunderstanding. Maybe Naruto is framed for something he didn't do, and the Konoha ninjas turn against him. In his desperation to prove his innocence and defend himself, he might end up accidentally killing some of them.
Perhaps there is a prophecy or some ancient power at play. Naruto discovers that by sacrificing the Konoha ninjas, he can save the entire ninja world from a much greater threat. He is forced to make this tough choice, knowing that it will make him an outcast, but believing it's for the greater good.