Honestly, one of the reasons I try not to think too hard on stuff like this: A ton of Western society was built on how the Church acted, and things they carried from Rome to Italy to Germany to France etc.
So you then it begs the question: How WOULD a Church be in a Pokémon world? Would it have accepted Pokémon as it implicitly does the existence and use of pets, farm-hand animals, etc? Or would it have rejected them based on some connection to non-Judeo-Christian religions? OR would it be a case-by-case reaction, based on, say, types, uses, etc.
It becomes FAR too big of a question far too fast, and far too outside the scope of a world like Pokémon. I know somebody who answered you referenced Arceus, but even it smacks more of at-best adapting Shinto ideas INTO a non-Shinto environment, assuming it isn't just a straightforward situation.
ANYways, as stated, the whole question is a bit out-of-scope for Pokémon, and ESPECIALLY this thread. Sadly it seems my request of a Luluco-Nervous-Eating edit was rejected, so I'll go back to just looking at what people post.