Edward Elric, because why not? First agnostic pope.
I thought he was an atheist? Or is that just in the 2003 anime?
Anyway, I nominate the asshole persona that Penn adopts when confronting people over their religious/supernatural beliefs.
I seem to remember his using the word "agnostic" in the manga (which, admittedly, I've only read a bit of - though he was an atheist in the first anime, yes, and I'm actually much more familiar with that version.), doesn't really matter though, he'd be the first nonreligious pope. Also alchemy could look like miracles. See the first episode.