The Horde should be extremely weakened after 5.4. The Loyalists and Rebels should both be weak and tired whenever Garrosh does go down, while the Alliance doesn't seem to be taking that much of a hit. This would be the perfect time for the Alliance to force a truce, and take back some ground.
The war will end after 5.4 and Alliance will be back to sharing the forefront with the Horde, no doubt about that.