There are somethings in the other books of the series which deal with trying to kill the almighty. It also introduces original sin, and other concepts like it

People just naturally think because something is called Daemon(old way of spelling demon) its against God but what those people dont understand its just a natural play-out of the story. The souls are called damons to explain why Ms.Coulter beleives they give us eevil horrible thoughts. Also because religon beleive witches are evil yet in this story the witches are good and help the hero. :P