I think it's something connected to either the Lifestream/Planet, or the Cetra. The fact that flowers grow there may support it. I also believe that the Shin-Ra may have banned religion and burned most worship sites, which is why this is the only church we ever encounter, and why it no longer functions.

I don't see how it could be even remotely connected to any real-world religions as Final Fantasy in in no way connected to Earth. The same goes for the church in FF9.