"Bread and Circuses" was not using code or lightly tapdancing around the meaning / identity of "The Son", which was integral to the episode's plot, not some random, out-of-nowhere reference pinned to the final act, which leads one to conclude Jesus and His impact on that world was a part of the drafts of the story right up to the final shooting script. As always, some are desperate to paint Roddenberry's entire life--especially the one he was leading when TOS was in production--as one of a militant atheist which influenced his imagined shaping of TOS, but the record says the opposite where his beliefs and intent were concerned. The episode in question is far from the series' only reference to faith, a specific being (e.g., in "The Man Trap", McCoy says, "Lord, forgive me" before Phasering Nancy) or Biblical reference, yet some continue to perform self-deceiving mental gymnastics trying to create an alternate history of the series which started / established it all.