Religion was obviously excluded from Star Trek because it would have caused unnecessary controversy. How could a show with a logical character like Spock or Data manage to land on some planet where there had been a visit from Jesus? How logical would it be for a Jesus to appear on Planet Omincron-5 in the Crab Nebula known by his English name? And if the Messiah had bore a different name, that would have been heresy. There were machines and individuals that ruled this or that planet based on myth and programming, and they were invariably exposed and deposed by the end of the show.
I do not expect religion, including Christianity to vanish, ever. They fulfill a need that some people have to be ruled by something other than logic and reason, especially because logic and reason vary rather widely between cultures when you get into political and social issues. Everybody can agree on the square root of 144, but not everybody can agree on "being their brother's keeper".
Religion will continue to change, but it will never disappear. Humanity will never live in a Perfect State, because change is an inseparable part of existence, beginning at the subatomic level.
If I were a Sci-Fi writer, I would not mess with any of the Earth's religions in any profound way.