I don't think their continued existence is too hard to justify. I'm enjoying the "narrative" of an alliance NE demon hunter - Having defeated the Legion, he was doubting his allegiance and purpose until the Teldrassil was destroyed, after which he saw the Horde as the major threat to Azeroth.
Of course, I also went with Altruis in Legion, preferring the "honorable, we-aren't-all-illidan" angle over the "succeed at all costs" that Kayn prefers, and protecting innocents from evil through a fight-fire-with-fire approach fits pretty well.
Questing through Drustvar as a DH is basically like RP'ing a Witcher, hunting monsters as a monster yourself.