Well, if it helps muddy the waters any, I believe the original otaku were created by Mirage, the AI that grew out of the Echo Mirage program.
Also, Deus was what his creators forced him to be. I always saw him as a Magneto-style villain. The whole shutdown thing, and everything that happened later, was done for one simple reason: survival. Renraku did the equivalent of putting a kink bomb in his head, and what follows was Deus doing everything in its power to get rid of that kink bomb, and make sure that no one could ever do something like that to him again.