Berman is senior to Braga, so he would have the final word on goes into a script. Not that it matters, atheist sci-fi writers are surprisingly willing to often stick either outright religious experiences in their work or at least something that is open to interpretation by the audience of "is it religious or something explainable being attributed to religion?"
Ron Moore is an atheist and he wrote the script for Rightful Heir, which is sort of a Second Coming story, not to mention he developed the story for Barge of the Dead, a portion of which is actually set in Klingon Hell. And then there's BSG in which religion, prophecy and chosen ones were very much part of the central theme.
Outside of Trek, sci-fi author Robert J Sawyer is an atheist and his work is considered by many to be "hard science" yet he typically inserts religious material into his work. Granted, most of the time it's science triumphing over religion, but there are a few times where it borders a bit too closely to being open to interpretation where he's almost flat-out suggesting a higher power definitely is involved. His novel Fossil Hunter actually does have a sub-plot told from the perspective of a god-like entity.
In Doctor Who, former showrunner Russell T Davies is an atheist was frequently inserting religious imagery into the show, most infamously by having the Doctor save the say because humanity had faith in him in the episode Last of the Time Lords. I'm not sure the religious beliefs of current showrunner Steven Moffat, though considering he depicts Christianity of the future turning into a military force as being the only way to stay relevant to human society, I don't get the impression he's very religious. Yet he frequently has religious-themed episodes or story arcs, most recently an entire season's arc was about the afterlife, though with a very atheistic ending to it.
I definitely reject the binary choice idea. What passes for my belief system is based around not making a choice!
