I've seen the scene quite recently. "Not sun in sky but Son of God", she has to say that. "Not sun in the sky but Jesus the Palestinian rabbi", does not make sense if she is attempting to explain the sun/son confusion. And yes, they were glad about it, and at least Uhura and McCoy thought very highly of Christ." And so do I. But I don't think he was a god.
From the production perspective, it certainly was a something for the Christian audience of the show. But that doesn't mean that the characters in the show were Christians.