Edit: Ninja'ed
That's a Very Good question. I believe it was because Menma lost his family, which is why he wanted the Red Moon Scroll, or so I think.
Except that Menma could have stayed in Konoha, gone to his family, and have shouting match with Naruto. After they were satisfied with Naruto's words about alternative reality, Menma and his family could have come to some truce and found the scroll eventually, or not because Naruto wanted to stay in that reality and decided to make sure the scroll is never found, thus making him the Villain.
Even if he eventually decided to go Back.