I agree with all three of you.
I think the episode treated religion somewhat better than TNG did too. In this episode, we at least get an acknowledgment that religion played an important role in the culture's social evolution towards scientific enlightenment. And the people actually embrace their religious heritage and are not ashamed of it.
On the other side, the only portrayal of religion that we get is rather negative. We see a culture in a Dark Age where heretics are killed and a glimpse of a 21st century society with the stereotypical megachurch preacher. So the final message of this episode seems to be that religion is a wacky but intermediary step in a culture's development towards true scientific reason and progress.
Also: the game with Bortus
and Kelly (wisely) ending it with Ed were really well done.