Sure - I totally get what you're saying. What I'm saying is that it makes for interesting drama in a TV show if you have characters having this argument in much more dramatic fashion. That it would be really really fascinating to see conflict arise over these issues on a starship where you really can't get too far away from the people who are bugging you about this stuff (religious or atheist). Maybe even go so far as to have a fundamentalist character that everyone else needs to tiptoe around.
My argument is entirely based on how interesting this would be to see play out as a conflict arising between characters.
We see things like this occassionally, for example Worf's Klingon beliefs or the whole Bajoran religion thing DS9. However, regardless of their personal beliefs the Starfleet officers are rational, scientifically minded people and tend to put their duty first. A person who cannot do that do not belong in the Starfleet. Of course, such conflicts can be better explored with new aliens and other non-Starfleet quest characters.