The main scene I remember where one of the protagonists resorts to torture is in the final season where Peter tortures a captured Observer to figure out how to put together a time portal stabilizer the Observers are using for transport. But if I remember the scene correctly, Peter doesn't even want information - he's just really pissed off at the Observers for killing his daughter. Even though this scene shows one of the protagonists doing something wrong, I question whether it was really trying to get the watcher's approval for the his actions. If anything, it was trying to show disapproval for his actions by depicting him as mentally unstable. I'm not saying that there aren't more scenes where the protagonists resort to torture, just that I can't remember them.
A further question that I have is what exactly torture is in a sci-fi show. There are at least two episodes where the Fringe gang uses a device that reanimates a recently deceased enemy so they can get the necessary information to stop an impending attack. Is a scenario like this torture? And what about when one of the Observers attempts to read Walter's mind causing him a great deal of pain? This seems to be torture, but would the shows viewers think that governments should torture because Fringe depicted a character reading another character's mind?
Finally, Ntrails makes a fantastic point. Typically, torture is not depicted as a critical story piece in Fringe. Torture occasionally makes appearances, but many of the shows fans can't even remember when and how often they were used. What does that say about the "legitimizing" force of depiction of torture in Fringe?