Yes! I will gladly discuss THE FFT with you. It's one of my all time favorites. I almost bought a PSP just so I could get The War of the Lions. But on to your question...
My understanding is the similar as yours. I see Ramza as the "savior," but I think St. Ajora was just a weapon the Glabados Church was using to obtain their goals. It's hard to say who the "main villian" is. I would almost venture to say there isn't one. There are many enemies with differing agendas throughout the game. Although if I had to pick one it would definitely be, not a specific person, but all the powers that be in the Glabados Church. They saw a struggle for a power in Ivalice and wanted to be the ones in control when the dust settled. And this brings me to your second question: I wouldn't say it is necessarily "anti-Catholic," but I do think it has many similarities to the Roman Catholic Church during the Holy Roman Empire and such.
It's late and I'm tired, so that's all I can spew right now, but let us continue this discussion.
Edit: Boo, why did you delete it?