If anything, Sasuke will assault Roots and kill Danzo. Itachi was obviously under Danzo's orders. Even Madara acknowledged that the Third was opposed to segregating or assaulting the Uchiha. The whole Senju/Uchiha rivalry thing sucks, but times change. Even Tsunade sees Roots as an enemy.

I think this all paves the way for Sasuke eventually rejoining Konoha, possibly as a spy for Madara.