What if I don't kill the Enthralled Wizards during the Morokei quest?
You'll be fine. You found a bug in the quest scripting, is all. The intended behaviour is that you have to disrupt/aggro and fight the Enthralled Wizards, which then releases Morokei, but there's nothing in the quest or rest of the game that relies on actually killing them. The rest of the quest triggers off of killing Morokei and getting the Staff.
Though, you did miss a pretty sweet boss fight.