I know I’m late to the party, and this seems fairly well-resolved, but I don’t see any reason Faith and magic shouldn’t be allowed. Mechanically, the two focus on different mediums - most common uses of Faith are to augment and restore, most common uses of Sorcery are to affect external forces. Aside from the heavy mojo workings of high Faith and Sorcery, the two barely overlap. In addition, most low-to-mid (available at character burning) Faith workings can just as easily be created with Enchanting - and those can be rendered permanent.
The two can be combined in a munchy way, but the can also be combined to create a very interesting, complicated character. The rest is just trusting a player to police themselves (or, if you don’t trust them, keeping them on a short leash).
I’d sit with your player and get an idea of his motivations. If it’s to create an elaborate, three-dimensional character who combines Faith and magic to accomplish his goals, then allow him to build his character and keep an eye on him to make sure he’s not exploiting the system. If it’s to create a human cannon, suggest he look elsewhere for his build, or put it to a group vote to outlaw it.