One of the most intriguing things about Pan is... it's him telling you to get the Gauntlet from the Dark Knight. Not Zobek. In fact, Zobek seems almost surprised by that turn of events (and pleased, for reasons made obvious by the ending).
However, in the ending Zobek acts like you getting the gauntlet was his idea all along. And if Pan is good, how does that make sense?
It's hard to imagine Zobek and Pan working together (even if Zobek's statement that he is "an old friend of Pan" is part of his charade); they seem to go towards completely different goals.
If anything, it's quite clear that Pan knows more thank Zobek does, and almost certainly he knows who Zobek really is and how Gabriel is being manipulated, and more importantly, he knows about Satan too - he's basically training Gabriel to fight him, very specifically.
If Pan is actually by God's side, why doesn't he warn Gabriel about Zobek? Just like Marie, he has faith in him and doesn't want to shatter his resolve? But more importantly, why does he push Gabriel to get the gauntlet, if that means basically making him Zobek's bitch?
I wouldn't go as far as calling it a "plothole", but Pan's role is definitely the most mysterious in the game.