Well, Sasuke has a trump card that (according to Suigetsu) would allow him to seize control of the war. Kabuto may have lost control of his (Orochimaru's) master trump card, Madara, but you can bet that Orochimaru had things planned a bit further/better, and perhaps Kabuto merely wasn't privy to those plans when he hijacked Orochimaru's powers for his own.
On the other hand, Sasuke is now in a position to capitalize on whatever Orochimaru was scheming. And while Sasuke is questioning himself, Itachi, the village, etc... he still hasn't exactly given up his hatred. Just because he wants to understand his situation doesn't mean that he'll see it the same way as Naruto. Imagine if the Ninja War ends, but the Shinobi system is still in place. If Sasuke arrived at the conclusion that the only way to provide justice for the world / his clan is to wipe out the corrupt Shinobi system (which necessarily entails destroying it completely), he may continue his plans.
Kishi will find some way to make Naruto and Sasuke fight, and it'll be the climax of the series, far greater than this skirmish with Obito/Madara.

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