I don't think he'll be corrupt. But Blizz did say Wrathion's goals differ from our own. He could try something like putting himself in charge of both factions.
Kosak has stated that Wrathion does have Azeroth's best interests in mind, but those interests might align with our characters interests. In his most recent interview I recall him saying that perhaps Wrathion thinks that Azeroth is better off with just one faction and that's why he's playing the Horde vs Alliance.
As for Wrathion ruling both factions....not his style. Wrathion. Sure Wrathion commands his Black Talons (who should have a more prominent role in MOP IMO) but that's it. He's fine with that. He likes working behind the scenes, he is a rogue after all.