Ehh, the lore has been bad for a while. I've been disappointed with lore since Cataclysm =/. Just try not to look at it and hope for the best, or if you're comfortable, abandon all the money and time you spent in this game and look for a new one.
The alliance needs the horde in the upcoming dangers, Varian although not a very brilliant conqueror will realise it soon enough. I do believe Varian was always trying to diplomaticly resolve the tension between factions through peace, mostly because of old Jaina, it has also been confirmed that Varian was negotiating with Lorthemar about the blood elves coming back. I think that by aiding the horde , Varian realises they may hold a truce for both factions to recover. However it does not rule out the fact the next warchief will be like garrosh in terms of agenda towards the alliance. Obviously ashenvale will still be attacked, and the forsaken will still keep things in motion over the plaguelands, we have yet to see a finale for that.