Exactly, if MoP didnt have the balls to actually make Orgrimmar hostile to the Horde despite it supposedly being actively hostile to dissidents then I fail to see how it would be different for Stormwind.
At most we will see the same as what happened to Orgrimmar. Stuff will be weirder than usual, NPCs will be accosted on the street, and maybe with the ability ot rescue them, and some guards will be snarky. Then we will get a dungeon, or raid, or whatever that has us go into a completely hostile Stormwind with the explanation that while we were somewhere else the complete takeover happened, and that when we return everything is back to normal.