At the end of Bread and Circuses...
... Uhura points out that the "Sun worshipers" were really "Son worshipers" and then Kirk waxes eloquent about how neat it would be to watch Christianity defeat Rome all over again. This is most I've ever seen a Star Trek episode talk about an Earth religion, and the reflection seems nostalgic and even seems to hint at a fondness for Christianity.
Given that we know Roddenberry didn't want religion in Star Trek and so on, what's the deal with this ending? Is there any backstory about why they would put this in? It is a clever twist which might justify the overall concept, but it's the tone that seems weird here. Were they under pressure to make the show more Christian-friendly? I note that the episode right before this was http://en.wikipedia.org/wiki/The_Omega_Glory in which natives decide Kirk is a deity... maybe they were trying to diffuse criticism?