In the original miniseries, Tricia Helfer exercises supernatural powers to murder a baby, for some unknown reason, an a dense crowd, yet get away with it. I suppose you could thus argue that showing us a Satanic monotheist slaying innocent religous pluralists (like US,) was foreshadowing the hand of God annihilating the anti-polytheists (which if we care to think about it very much means anti-Trinitarians.) In that sense I suppose that we could agree that a heavy-handed and bigoted religous theme was there from the very beginning.
But why then did the series go out of its way to also foreshadow an ostensisbly "rational" science-fictional alternative? In particular, the series absolutely insisted on the denial of a soul to the Cylons. Their immortality was based on the transmission of memories. Of course, the series also insisted that Cylons were indistinguishable from human beings (Baltar's detector was left ambiguous by the end.) This means that the show insisted that Cylons sent data without a transmitter! Such nonsense is perfectly acceptable to incompetents who have no sense of style in fictional science. The important point is that the show relied to the end on simultaneously foreshadowing a totally "rational", i.e., nonsupernatural universe.
Unfortunately, it is unlikely that anything, not even the finale, with bring down the internet shibboleths about the 9/11 BattleStar Galactica.