It's interesting to think about Katrana being removed from Stormwind, but I doubt it. Maybe the story will be that she successfully hides her involvement in the scheme until the player does the quest lines, and at the part of the Onyxia attunement quests where dragonkin now attack Bolvar in the throne room, they'll attack Varian himself. And going after Onyxia will be about avenging his imprisonment instead of rescuing him.

The reason I doubt Katrana will be removed is that it would be a very big change. At least two long quest lines spanning a dozen zones would have to be deleted or changed completely. Her deception ties into what the Defias is doing in the Deadmines and what Nefarian is doing in his lair. Sure, those instances would still exist, but it would be hard to swallow them remaining the same.

Have the game designers ever taken any content out before? The announcement that they'll move the existing Naxxramas — one single instance that very few people ever entered — is the only example I can think of, and even that seems like a much smaller deal content-wise, and seems to cause no problems at all lore-wise.