At this point I don't see a 3rd side ever happening. It would simply require too much restructuring of the game, much as Gisli said.
I'm not really sure that there would be an acceptable way to do it without limiting it to only three armies. Though, in truth, the Destruction armies would never be allied in the way they are. You can sorta consider them a "faction" and be supported by the back story, but the actual side-by-side fighting isn't. It's one of those times where lore needs to be sacrificed for gameplay
I will certainly be playing Destruction, though, as I am a big fan of the Dark Elves and really want to play a Disciple and my friends are also quite attached to various Destro races/classes.
"Oh, hell no," Kylar said. "You cannot fly. Tell me you can't fly."