I don't think that this should necessarily be considered a spoiler, but just in case I find myself on the wrong end of a drunken Pubrick later, consider this ample warning...
Edited before posting (but couldn't bring myself to remove the above): I actually probably deviated into more SPOILER territory than originally intended. You have officially been warned.
I've read the early version of the script. There may be parallels to Scientology, but at no point did it seem to be about Scientology. To me personally, it seemed like an extension of the fundamental Christians depicted in Chere Mill. Really, though, it's more a generic cult. This film will speak more about religion in general, rather than Scientology specifically. I don't want to call it satire, but in a way that's what I took it to be. He's holding up a mirror to all organized religions, but making it more accessible and palatable to the masses by having it focus on a small group, a cult. That's my take on it anyway. But no, I haven't read the shooting version of the script.