Does allying with one side lock you out of promotion quests or other content?
Solution 1:
The answer is "no". As soon as you pick the side, other's side world NPCs become hostile, and in-house NPCs refuse to talk to you, so shops and promotion quest is locked out. It is true for dragon-dragonhunter quest and necromancer-cleric quest both. It is quite possible to promote everyone long before you have to take a side, though.