Well, Pope Benedict IX is an actual historical figure... Must be some reference to past Doctor Who, perhaps before the 2005 series, because I have no recollection. Or I guess it could be one of those middle of the nowhere, never previously seen things that this series likes to do sometimes.
So the pope appearing in the episode was the modern one in the Doctor Who Earth. Perhaps that clears up why he wasn't speaking Latin. Not that I know enough about what language a modern pope speaks in. Still seems weird that the TARDIS wouldn't translate it, though.