WoW won't end the Warcraft universe, and I believe it's been stated that most events in WoW aren't considered Canon changes to the plotline.

There are still several commanders in charge of the Burning Legion, Arthas is (for now) alive, and Deathwing is still unaccounted for. Those are all old villains that don't really even need a cheesy "return" to be a threat (like having a cult resurrect Sargeras or something stupid).