I think it's obvious that D&D had Christianity as it's implicit religion and EGG removed references to it to avoid making people uncomfortable about the representation of a real religion in a fantasy game. I am pretty sure the whole "Satanic Panic" caught him completely off guard.
The people that should be pissed about religion in D&D are the Pagans of the world. My copy of the Deities and Demigods book lists American Indian, Central American, Chinese, Indian & Japanese "Mythos", which represent tribal gods of various North American Indian tribes, many of which are still venerated, Chinese Gods that have been adopted into Buddhism, Hinduism and Shinto.
Various "dead" European, middle eastern and north African religions are represented too, although they have adherents through either Wicca or Reconstructionist Paganism and their adherents number in at least the tens of thousands in the US alone. The only fictional religions represented are the Newhon Mythos and the Nonhumans' Deities. So only the big three Abrahamic traditions get a pass in D&D? No Judaism, Christianity or Islam, but it's OK to use Hinduism or Buddhism or Asatru?