Terry will explore the question of organized religion and belief much more effectively and fully in his later books, probably because Terry has thought more about society and religion. While organized religion and gods are a small part of the multitudinous elements of satire in this book, I think that part of the problem with the "gods" here is that he's trying to make them "Egyptian" (as with everything else--initial "P" tacked on to many names, some similarity to Egyptian gods). But I think it's probably important that we never hear any more about this land in all the other Discworld books.
I don't think that Terry is anti-religious (or not as much as you ex-Catholics seem to believe). I will agree that he is dubious about religious beliefs that call for organized rituals. It's not just the Catholics that he parodies. The Omnians seem to have (in later books) a distinct similarity to groups such as Mormons, Jehovah Witnesses and any of the other religions that do house to house calling. But in some ways, I think the book is more about the dangers of a theocracy especially when driven by a megalomaniac than an attack on organized religion.
The problem with Dios and his gods, it seems to me, is that he suffers from a
Narcissist Personality Disorder. Dios doesn't believe in gods, but he has created them as a means of manipulating people and uses ritual to enforce his decrees. He has effectively stolen the power of the god/Pharaoh by use of the golden mask (which interestingly turns out to be primarily lead). He is the only real power in the country and he has had 7000 years to indoctrinate his people. Dios can't allow himself to die, because he tells himself that there's never anyone to replace him at that time. Ironically, the high priest of the kingdom has no spiritual belief at all.
He says that he exists only to serve--and the sad/terrible thing is that he believes that. Unfortunately, the person he exists to serve is himself. He shows no care or concern for the people or for the welfare of the Kingdom. He has created all the gods that appear during the disconnect from the rest of the world to increase the amount of ritual and elegance in formal worship and as a means of control. They seem to be totally oblivious to both their priests and the fears and terrors of their worshipers. That's the reason the gods pay no attention to either their own priests, or the country and the reason that Dios can't really control them.
It seems to me that Terry is not anti-religious, but rather highly critical of almost all organized religions. perhaps, I think, because they can and are so easily perverted. The central core teachings of Judaism, Christianity, Islam, Buddhism and Confucianism are very much alike. I suspect many of the other smaller religions (eg. native American) have similar views of how one should conduct one's life--whether or not it leads to some kind of immortality or not. And in
Carpe Jugulum, even more I think than the other "religious" satires--Terry talks about what he believes. Sin--is treating people as things--at the simplest level. Is that so very different from love thy neighbor as thyself, or the equivalent precepts of other faiths?
I still say that
Pyramids is far from Terry's best book. (Sorry Pooh) But I will admit that there are more elements in it than just the clever "can you figure out this allusion" humor, which I find quite boring after a bit. But, I think there are too many things in
Pyramids that don't quite fit or are largely irrelevant. Terry learned and developed his satiric skills in the later novels (although I'm a bit unsure about the last couple). For example, I think that using the technique of having Teppic trained as an assassin does give us an insight into the society (and more to the point gives him an insight) that is a useful literary device. But I don't think Terry has perfected his control of this. This book feels a bit like "everything but the Kitchen Sink" and it may be there too. But there are indications, from time to time, of the really great writer Pratchett will become.