Having an actual duplicate religion in the game just doesn't work, because that would affect units, buildings, and everything that requires religion and basically would make everything very ugly.
I tried to only change the displayed text but that just doesn't work from how the code works.
So Orthodoxy it is even before the schism.
Alternatively, we could have the Catholic wonders as requiring (Catholicism or Christianity), Orthodox as (Orthodoxy or Christianity) and so on. Once the Schism happens, All Christian cities could be changed either to Catholicism or Orthodoxy, being the only case when a religion is wiped out entirely, probably even including its Holy City.
Besides, I saw that Jerusalem is the Orthodox Holy City in the 600 AD scenario and I believe it was Constantinople in the 1700 AD scenario. Is there a way that the Orthodox Holy City can be changed? My idea is that Hagia Sophia defines it. And back to Catholicism, St Peter's Basilica and the Apostolic Palace are different buildings. We could have the Apostolic Palace as the Catholic shrine and St Peter's Basilica as a wonder that requires it. Someone around these forums suggested the Churches of the Holy Sepulchre and Nativity as Orthodox and Catholic shrines. I liked that idea, if added it could be two shrines for two denominations.
And with this religion issue beyond Christianity, I saw myself having religious disunity as Khmer and China, when supposedly Buddhism + Hinduism and Confucianism + Taoism are tolerant with each other. If this could be fixed, I would like this to be considered in the future when Shinto is added.
Also, Zoroastrianism has few Wonders, while Protestantism has none. If we could just come up with a Zoroastrian wonder that gives a free Courthouse in every city or Administrative Center in every conquered capital it could help in representing the satrapies, while one that leaves no destroyed buildings in conquered cities could represent Cyrus's way of conquest. As for Protestant wonders, they would obviously be buildings as temples or cathedrals (ideas: St Paul's Cathedral, Westminster Abbey
even if it was originally a Catholic church, an American megachurch), because otherwise they would make sense as secular wonders.
And with all these religions added, we should reduce Spain's and Tibet's UHVs, since they could become near to impossible to complete for them.