I think there was another Star Trek episode that had an unmistakable Christian reference (although I might be confusing it with the same one you already mentioned - so correct me if I'm wrong.)
There was an episode in which the Enterprise encountered a seemingly primitive group of people who appeared to be Sun worshipers. Always referring to the Sun this and the Sun that, but near the end of the show it was discovered that they were not worshiping the Sun. It was the Son - Jesus Christ.
Was that a different episode or the same one you mentioned?
It was the same episode. IIRC, it was set on a planet where the Roman Empire still existed into the 20th century. It's the only time I can remember where religion was ever even mentioned on a Star Trek series, although I didn't see all of DS9 or Voyager and almost none of Enterprise so I might be mistaken.