The episode doesn't posit that the deity they believe in is real. The most you could say about it is that Kirk and co. preferred religiosity to the cruelty and oppression of the status quo, playing into Gene's idea of human progress towards a more compassionate future. This, of course, ignores the negative influence of Christianity over time (like the crusades, inquisition, or most relevant-- resistance to science, of which, we're still suffering).
Well said (written). Thanks.
I don't even think we can infer that they "preferred religiosity." They just seemed interested in how the myth would evolve on that world. Would history there diverge from Earth's history after Christ's time, or would it be the same?