Konoha's leaders have been elected by Konoha itself. Like in a democracy, the citizens are responsible for the actions of their leaders. Even if they later depose those leaders, it doesn't change anything, unless the victims forgive them. Naturally it's fell to slaughter everybody in response, I'm not saying it wasn't, but that's only so in Naruto's new type of ninja world. Perhaps Itachi was starting to think so before the end. But Sasuke is still living in the old world, unless Itachi managed to change him, who knows.

Anyway, my original point was that it's hasty to think all villains would form a united front. Why, we just saw Itachi & Sasuke bring down Kabuto's army of the undead, as well as Kabuto himself, for he won't be his previous self anymore if he intends to escape Izanami. Kabuto, Tobi, and Madara didn't see that coming. It might even serve Sasuke's purposes to see this war end soon so that the allied ninja army would disband and Konoha would be ready to receive Sasuke's greeting. If Madara wins, there might not be anymore Konoha for Sasuke to defeat. That might be a bit unsatisfactory for him.