1. Yes, I've never had him go hostile. Maybe you hit him with an AOE spell during the fight and turned him hostile?
2. Yes, I've never seen any parasite scuttle away too fast. I don't think this affects anything one way or the other story-wise.
There isn't a time limit as far as I know but long rests do sometimes affect things. Bit of a spoiler
There is no fighting at Waukeen's Rest just lots of fire/burning.