Star Trek is about the future of humanity and of exploration, (well it used to be). The last thing Star Trek needs is to return to the dark ages of the military, fear, superstition and doctrine, something that has emerged of late. This is starfleet not the Royal/U.S Navy. Starfleet was founded to seek out and explore in peace, not exploit and conquer in war.
Since the end of TNG the franchise has slowly slid into a militaristic side show.
to quote Jean luc Picard "Does anyone remember when we used to be explorers"
If someone needs religion they don't need a priest/chaplain
I would have thought we were beyond such nonsense ...