This raid isn't like SoO where Anduin goes rogue, this is a Alliance vs Horde raid. As was hinted at during Blizzcon, there's no reason we can't have Alliance vs Horde raids.
The Horde takes the role of sieging Stormwind, and the Alliance fight them off. It's the same raid, but each side of the conflict is completely different. Think of encounters like SoO but each side of the conflict is different, ending with a climactic battle between Sylvanas as the Alliance boss, and Greymane as the Horde boss.