I think (with the caveat that I've read a lot but not all of the sequences) that it is Yudkowsky's position that religions are specific manifestations of a whole cluster of more general failures of rationality, and that once someone truly internalises all of the best techniques for separating probable truths from probable untruths, it will be more-or-less impossible for that person to remain religious (unless, of course, they are sitting on a mountain of evidence in favour of the existence of one or more gods which has not been made available to the rest of us), and that it will be <i>obvious</i> that the specific claims of religions are false.

So yes, there is not much in there that explicitly rebuts the god hypothesis, but probably the closest thing to what you are looking for is <a href="http://lesswrong.com/lw/1e/raising_the_sanity_waterline/">Raising the Sanity Waterline,</a> which lists the ideas that ought to make discarding religions into one of the low-hanging fruits of any attempt at upgrading one's rationality.