well, I'll throw in my 2 cents, I suppose. Dream topic for me, you could say...
In no particular order of general points :
Even commune, does not (IMO) require an actual diety. Mechanically the spell can work exactly the same with the flavor text changed. The cleric expands his mind into the realm of omniscence, kept focused and sane by the mental exercise of "talking to his diety and asking a question". Considering the overlap in effect, but complete difference in flavor text between meditation, hypnotism, prayer and easy listening music, its not a stretch at all. In fact, atheism could easily be the default for non-alligned clerics. "Yes, I suppose its easier in some ways for you to form your powers out of a premade framework and the belief that you are merely channelling another... Intellectually lazy and spiritually stunting, but if thats what you need to do the work, well, it works for you...."
Atheism does not require an explaination for "supernatural" events. It requires only that one consider "god" to be a less satisfactory one than "I don't know".
I would boil down the major confusion over definitions of gods and call a god "a being worthy of worship". Atheists do not disbelieve the sun or the emporer of Japan when encountering people who worship them as gods. And yet, even when someone defines "god" to them as "the sun" they don't stop being atheists. So a person in a standard D&D setting who veiwed the gods as "merely" powerful beings who mucked in human affairs would IMHO be an atheist. Anyone who thinks that's too much spliting hairs on the semantics of the words should spend half an hour on alt.atheism. Or not, your head might pop from the layers of definition that go on there.
I'm a big fan of the "gods created by their worshippers, not the other way around" theology as a basis for fantasy. Most of the populous and even the gods themselves don't have to be aware of that relationship, of course. (Small Gods is a must, IMHO if you are looking at alternate theologies for your worlds.)
If you haven't heard of the God of the Gaps theory, its very applicable to this sort of conversation. If one is inclined to believe in g/God(s), one will find that unexplainable gap to put it/them in. If one for whatever reason is not so inclined, no gap it too big to hold open with an "I don't know yet" to stop g/God(s) from slipping in. To assume that an atheist in a D&D world must be a crackpot is quite frankly lack of creative thought. It could easily be the default of wizards and druids.
Final thought - From an internal D&D world view, how could you convince a sorcerer who thought his powers were divine that this wasn't the case? Or a Bard who psychologically could not cast spells except through hymns?
Kahuna Burger