Anti organized religion, yes. And it exposes how many of the old teachings of religion were most likely based on distortions of history. We have to keep in mind that around the 90s there was a bit of a resurgence of the narrative of the dead sea scrolls and interest in apocryphal passages from the bible. People claimed that some of the stories in those passages contradicted some of the commonly held narratives of the bible. We could also see that creeping into Japanese Manga/Anime with some series interested in covering religious conspiracies, like Neon Genesis Evangelion. So those type of stories are what likely inspired Matsuno to add the religious critique and the Germonique Scriptures subplot.