As I said, this doesn't break the social contract - I brought this to the magistrates only because it's not clear who this kind of thing should be brought to. The player of Perrin has been playing since 2006 - he should already know that atheist characters aren't allowed. If he'd been a new player then I wouldn't have brought it out of game. But, as it is, I think it would be fairly fun if tom were to decide to bolt the character - it would probably be good for gameplay.
That being said, I'm also perfectly happy if it's decided that this isn't something which should be taken out of game and which should only be dealt with IG. In which case it can act as a precedent for future situations like this.