Isu was just what the devs made up as the creators of the world, not something they actually place as "God" in their franchise? So the devs just made their own "book of genesis" and altered the events of Creation? Just a question
Going back to the very first AC games, Assassins and Templars alike are skeptical of conventional religion. The existence of Those Who Came Before (as they were originally called, what a mouthful) basically discredited everything except for the actual creation of the universe.
Dive into the lore from ACII/Brotherhood/Revelations/III and you will see specific examples of the series explaining modern religions away (ex. The Truth video). They created us and the tens of thousands of years that have passed since the Great Catastrophe have turned them into legends and gods. But who created the Isu? That's still unanswered.