tl;dr version: The writers can do whatever they want, and personal beliefs that science and religion are mutually exclusive are flawed since nobody's disproved the validity of religion, and many previously religious ideas ended up being accepted as facts and understood through scientific terms. The jury's still out on it, and any other opinion is that of a myopic, close-minded individual.
For those without ADD:
As a writer, I'm a little saddened by the ridiculous notion that's been repeated about religion not working in sci fi. It must be understood that, within the context of a fiction, the writer has full control. If someone writes science fiction, but includes religion, themes, and/or subtext, their story cannot be suddenly ignored as not being science fiction. That stems from an idea that religion and science are mutually exclusive, and many noted scientists, such as Newton, Copernicus, Kepler, and so forth, would doubtless beg to differ. One of the lead researchers on the human genome project actually became religious after what he learned about the human genome.
This idea that the inclusion of religious beliefs into genuine science is one thing, but what's worse is the idea that one cannot blend science and religion in a fictional work. That, to me, is utterly ridiculous. I once wrote a story, and a certain individual who read it didn't like something that happened, and told me that I had to change my story to fit how he thought my story's world should work.
It doesn't work like that. You don't tell the writer how to write. He tells you what happened in his fictional universe. Few things make me angry, but the gall to assume that someone who is not as intimate with the fictional universe somehow possesses more knowledge than the creator fills me with a passionate rage.
Dana Scully's Catholocism and Frank Black's struggles with evil did not magically null the validity of the X-Files and Millennium as Science Fiction. While it's more likely than not that we are the only form of life out there (Monkeys eventually reproducing Hamlet have a better chance than our evolution), lots of Sci Fi is about alien life and fantastical technologies that are scientifically impossible, but no one would call them "fantasy." If Asgardian gods suddenly showed up in a book about space ships and time travel and aliens and improbabilities, I wouldn't call that fantasy.
...I'd call it the Hitch Hiker's Guide to the Galaxy.
Science Fiction is fictional and is not an exact representation of everything we know to be true; in many cases, elements of science fiction are downright false. Religious elements within science fiction are perfectly acceptable and do not alter the genre in any way. ...unless elves and dwarves start appearing; then everything gets a little suspect.
As for society devolving and the like, the Mormon beliefs of the show's creator make sense here. After all, according to Mormon doctrine, a group of people migrated from the heart of civilization to the Western Hemisphere, some of whom became savages (namely those who didn't create a written history of their culture) and some of whom became the Mayans, one of the most advanced cultures on Earth for its time, if I recall. Besides that, facilities, books/information, tools, and the like are all required to train people in certain paths, and those resources would, understandably, be lost over time without the proper facilities to maintain them.
(I posted after reading all the way through the first page and only a few comments on the second, so if I've unnecessarily repeated anyone's thoughts, I apologize)
