I'm not sure but the locked doors in the inn should be the fighting pits, if so there should be no-one inside. I'm guessing you overwrote your autosave when you went into the inn... tricky situation have you done mr.pirate/lich quest if not you may need his runestone to get to someparts of the city where there may or may not be more drow. To be honest I don't know
Bhaal I once had Jaheira's friends attack me whenever I left the underdark causing the elves to go hostile... I feel your pain!