Board Thread:Assassin's Creed general discussion/@comment-26314858-20150714112803/@comment-2112031-20170725213715
I too had written a crossover quite a few years ago between Star Trek, Stargate, Doctor Who, Assassin's Creed and a couple other franchises. I made the Isu the same race as the Ancients from Stargate and the Ancient humanoids from Star Trek.
In terms of AC lore, based on various statements made throughout the series, it seems that the Isu are indigenous to Earth and evolved there. At the end of AC2, Minerva specifically refers to Earth as "our home". Not to mentioned the aforementioned fact that, if they aliens, they could have used whatever spaceships brought them to Earth to either leave or at least use them as shelter.
Assuming that Abstergo's classification of the Isu as "Homo sapiens divinus" is accurate, that means that they are a species of the line of Great Apes who naturally evolved sapience and eventually became the dominant species on Earth. It is specifically mentioned that they genetically engineered humans from a pre-existing primate species, probably because they're closely related to each other. Their ability to interbreed with humans and produce fertile offspring further confirms this relation.
As for their religion(s), if they developed naturally, it would probably mean that they also developed hundreds, if not thousands of different religions over the course of thousands of years of history. By the time they created humanity, it seems that they had mostly become secular, with no explicit mentions of any beliefs in supernatural beings.