I let the Vithrack live in the Engwithan ruins under the lake. Did I give up my only chance for a "soul vessel" to complete the quest with the stone heads?

Yeah, you only can loot it from his dead body.

That thing is a Vithrak? Been looking for its brain for many moons now. Its benevolent to let it go but...I notice in this game, a lot of enemies I should be killing I usually end either letting them live or *helping* them. I remember recalling after entering the catacombs, 'thats the 2nd time I've come across a necromancer in his den, surrounded by his minions...and didnt kill him...now Im off to find a grimoire for him?'

Osyra almost fooled me as well.

Almost.