I didn’t think it was saying the Yangs were superior. I thought it was saying their declaration of independence - their ultimate system - was superior.
TOS did more than one hint at religion. Remember the Sun worshipers in “Bread and Circuses”? In the end, on the bridge they were sort of mocking the Sun worshipers and Uhura said (IIRC), “I’ve been monitoring their transmissions. They don’t worship the sun. They worship the Son. The Son of God.”
There were a lot of moral and political messages in the show and it was very, VERY conservative by today’s standards. Sometimes they were heavy handed enough to ruin the episode.
Did the German tribes take over Rome? That confusion only makes sense in Germanic languages and not Romance ones based on Latin.
There is another episode ("Who Mourns for Adonais") in which Kirk says something like "We've found the one God to be quite sufficient."
Yes, they were much more respectful of religion in the 1960s.
Gene Roddenberry was just another secular humanist whose ideals were all groundless because they weren't based on Divine Law.