Pretty sure there's at least one place where an alien quotes Scripture, or at least uses an English-language idiom with roots in the Bible, but I can't put my finger on it. Kinda feel like Spock does in TOS but also that it happens in 90s Trek, but I'm not sure.
TOS has the episode “Bread and Circuses” with that 20th century Roman Empire planet which itself was starting to develop the concept of a monotheistic order and a concept of a scion: Uhura and Kirk both elude to it, which means at least Earth Xtian doctrine is known if not followed.
In "Far Beyond the Stars" Joseph Sisko quotes a verse from St. Paul. Benjamin says "I've never known you to quote the Bible before," and Joseph says "I'm just full of surprises."
Picard quotes enough Shakespeare there’s surely at least an incidental Biblical reference.
Uhura specifically called out the son of god in TOS on the Nazi Romans episode.