I've been a horde player since mid BC, but well, I have a toon in alliance as well. And based on my experience, horde queues for BGs are a lot longer than for alliance. Of course, more players in horde means more wait for a group of allies to gather around and queue for BGs.
So I think it would be possible and plausible that blizz could get both horde teams to fight each other. Just mask the oposite team as an ally team (like dungeons we have seen before), turning undeads into humans, orcs into dwarves, etc. That way, both sides will still be horde "fightning alliance".
That way, 40 horde players would not have to wait for a 40 alliance players to queue. They could instantly join a 20-20 BG.
What do you think about that?