Yes.
Legend of Legaia, but it depends on your definition of "pope-like figure"
SPOILERS
There are two old guys clad in robes that are most definitely on your side, but they're more monks than popes. There's also a prophet that helps you not once or even twice, but thrice throughout the course of the game, but he doesn't fit the physical description of pope- he's a baby- actually he's three babies that share the same mind but different bodies. And there's a God- a literal God- on your side.
END
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Need new sig