Unique theory, but my spider sense tells it most likely won't be true. All of the Uchihas are dead. If Obito was still alive I think there would be some sort of indication that there were more then just two uchilas. Plus why the hell would Itachi want to work for someone from the clan he despised and slaughtered?

I think that the head of the organization is a completly new quasi god like character whose probably very infamous in the ninja world.