A very nice justice system indeed. He never went to jail, the church took him to "take care of it's own". How's that any different?
That is because the story runs on another moral view. one where mercy is more important than justice. The first is seen as an opportunity to save souls and the second is seen surrendering to lower emotions like revenge, hate and so on.
Not always very practical and maybe less gratifying for normal people but if you want to wield one of the swords you need to subscribe to it.
Of course if someone threatens to blow up your daughter the most practical solution is to kill him and torturing him first might be emotionally satisfying but it is not good for your soul and his soul wouldn't get a chance to improve.
Besides there is a justice system and kidnapping is certainly something to lock you up for but the church is well known for ignoring that and taking it in their own hands. I would say that is wrong but I am not a knight or an archangel either.