Ah, but the "letter of transit" felt consistent with the movie's world,
Among other problems, the letters of transit are described as cosigned by General de Gaulle
. And one can't treat the reality of Casablanca as quite as arbitrary as a genre film. They are a nonsense plot device, pure and simple, and the film works in spite of them being nonsense.
Guilt certainly is not necessary for believable, interesting villains - my mind turns instantly to Akira Kurosawa's modern day adaption of Hamlet, The Bad Sleep Well
. Even if one hasn't seen it the title elucidates the point perfectly - some people really are not bothered by the ethical implications of their actions, and that lack of concern is part of what makes them a villain.
As far as belief goes, it's manifestly obvious that Ra's al Ghul believes that what he's doing is for the good of humanity, that corruption and decadence is a sin that needs to be purged. He's the most uncomplicatedly principled of the antagonists in the Nolan Batman films, which probably makes his role as an unsubtle terrorist stand-in all the clearer.