Well, in this scenario, Naruto joining Akatsuki would change a lot. Naruto has always been about hope and unity. In Akatsuki, he'd be surrounded by outcasts with different motives. His influence could either sway some Akatsuki members to his side or get him in a lot of trouble. He might try to change Akatsuki from within, to make it less of a villainous organization. But this would be really tough as many Akatsuki members have deep - seated grudges and goals. For example, Nagato might have a hard time dealing with Naruto's presence as Naruto would challenge his view of the world. And Konoha would be in a very difficult situation. They'd see Naruto as a traitor, and it would be a big blow to their morale.