Most characters that were re-done drastically were just replaced by new generations of the same hero. Hal Jordan and Kyle Rainer replacing Alan Scot for example, or the new Firestorm, Atom, and Blue Beetle come to mind.
Now, I havent read these 99 characters but the producer of the comic books says in the interview that he makes a specific point of not referencing religion specifically in the stories. These characters simply come from a different point of view than the traditional Judeo-Christian creations of North America from his point of view.
I am, however, genuinely concerned about the blatant ignorance of the Middle East coming from some posters on this board. Islam has as rich a cultural history and a myriad of interpretations and followers as Christianity does. Saying every Muslim is out to attack Western culture is like saying every Christian is a homophobe, a Nazi, or a member of the KKK.
Nobody defended Christianity here either. I certainly won't.
If you're a person that thinks religion is something to be seen with skepticism and that following an ideology that is based on falsehoods about the creation and nature of the universe then you must call it wherever you see it.