I've said for a long time that Rogues should be able to quest and be in dungeon queues for both sides. After all, Blizzard's own definition of the class says that the rogue is entirely devoid of loyalty to anybody except the person who is paying them at the moment, that the only law rogues obey is the law of the contract.
Of course in PvP they should fight for their faction, but I don't see why they couldn't quest for both sides or do cross-faction lfd/lfr groups. Would probably help out queue times at least.