Atheist VS Naturalist - the latter sounds more appealing to me...

[LadyForCamus]

is there a way to distinguish between a supernatural cause and a natural cause as of yet undiscovered?

Not that I can think of.

What I want to do is avoid begging the question, as poly does.

He says that even if there is a complete lack of naturalistic evidence, he would consider supernatural explanations to be failures. It would be "throwing up your hands" and accepting defeat. Even in the event of no natural evidence, he would just assume that there must be some. 

If you accept that it is a metaphysical commitment on your part that any explanation must be natural, that's fine. But it's not provable.

So, if there is no way to distinguish between a supernatural cause, and a natural cause that we’ve yet to uncover; if there’s no way to even assess the probability of one cause versus the other; and if up until this point, every cause for a physical phenomenon we’ve ever explained has been a natural one, what reason is there to think that the supernatural is even a possibility as the cause of anything in the first place? That sounds an awful lot like the same metaphysical commitment you mention with regard to philosophical naturalism. In fact, it seems an awful lot like a rationally unjustified presupposition. At least in the case of philosophical naturalism, we have enough examples that we can make an inference.