I doubt they’ll actually combine the Factions. I’d say that they’d become two cooperating nation states - like IRL. Just cos you are Allies doesn’t mean you become one Nation!
Besides, the Horde as a Council-led Faction vs the Alliance as a little boy-led Monarchy is a great dynamic to have! Both factions have their agendas, individual have their own disposition towards faction hostility - its two takes on how the next threat will be dealt with.