The idea of a machine race developing religion seems rather implausible to me; the Cylons don't need an origin myth: they already have one. That was one of my problems with the miniseries, and it doesn't appear to have gotten any better in the series: the Cylons seem to be decidedly irrational. ...The Cylons had to know they were on the verge of eliminating the last remnants of humans in their part of the galaxy after a week of chasing them, so why not just resume that until the humans break down? Obviously that would make for a lousy series, but it's the kind of question I think should be answered to maintain suspension of disbelief. Perhaps the creators have a longer-term plan that will explain all this, but right now the Cylons' motivations seem to be highly incongruent with their actions.
An explanation would be: when Number Six is talking about God, I don't think she's talking about a Judeo-Christian omnipotent, omnipresent God; I think the Cylons have developed the equivalent of a hive mind. She gets instructions from God, she knows directly whether he's angry or happy.
The other part is, I don't think the Cylon's main goal is the extermination of the human race. I think they want to find out what makes humans tick, and are doing it like a child disassembling a toaster