It's way easier to ignore the church than it is magic in DnD, for one you don't stumble into special weapons and gear that in DnD would be magic, or at least we didn't.

What I mean is that there are no mechanics tied to the church/religion unless you were a member of the church(although this wasn't the most recent edition, maybe things have changed).

In our game the pc's probably would've been labeled heretics but nobody cared. The adventure took place in a random system with very little church presence, they were easily left as a background element.

There are entire sourcebooks on battling sentient alien plant ppl, those I remember. Religion never really came up, the only special power thing was a psychic.

I just chafe at the "really meant to be played ..." attitude as it works great without religion being involved at all.