Not a bad article overall. I didn't read future toddler chopper Vox Day's original article, and I'm sure the guy defending him is an idiot, but I do have to quibble with some of your statements.

No, correlation does not imply causation, and a hypothesis should be generated before any experimentation is undertaken. The hypothesis comes from pure observation, and is then proven or not by experimentation.

This is not quite accurate. First, the commenter seems to mean "implies" in the sense of "suggests", which is reasonably accurate. Furthermore, hypotheses are generated all the time, in response to observation, experiment, intuition, or just plain guesswork.

these things are only observed within the natural world and the supernatural is a priori excluded.

It's more accurate, I think, to state that the word "supernatural" is incoherent and meaningless. It's just a fancy word for ignorance.