Even though I am an atheist, what I'm about to say is purely from a dramatic, storytelling perspective.
Religious stuff is interesting when both sides have leverage and points to make, when certain things definitely occur but WHY they occur and how you can put a spin on it religiously are up for debate. DS9 (the Bajoran religious POV vs. the Federation's atheistic one) does this well as does A Song of Ice and Fire (you've got R'hllor, Old Gods, the Seven, Many-Faced God; or are there just elemental ice and fire magic that humans attribute personalities to?). Is it religion? Or science? Who's right? These questions are raised and moments are made in favor and against, but they're ultimately left as a neutral area, allowing us to make our own decisions.
BSG's religious stuff got dull when God definitely 100% existed and could affect the plot. It just kills interest in the story stone dead. Early S1, you have polytheistic humans, monotheistic robots and a guy talking to a girl in his head who may or may not be real. Again, this is interesting. But it stops being interesting when the narrative takes us aside to whisper, "P.S. The Cylons are the right ones," and then are given a giant question mark plot device that can do anything and everything at RDM's convenience. If a weird plot hole develops between S2-S4? Err, God did it. BSG was an excellent show for much of its run (especially the early years) and there are many reasons for that, but I'd use it as a prime example as how NOT to use religion in a show. It sucks all the fun out of it and leaves it a giant plot vacuum.