A point you repeatedly make in your OP is that everyone uses torture -- not just the bad guys -- and that it's just a tool to extract information. So it seems certainly relevant that your selection of examples are all of bad guys committing torture on the "good guys" or otherwise innocent victims.

Fringe, especially in its earlier "monster of the week" seasons, has a very clear distinction between the "good guys" and the "bad guys". Since only the bad guys are committing torture, it seems more plausible that the writers of Fringe think that the audience will view torture as something bad people do. However, it does not support your point that torture is a tool used by everyone.

There's one plot line in season 5 where Peter tortures an Observer. But it was depicted as a moral failing of Peter to commit torture, opposite what you suggest in your OP ("In fact it’s often portrayed as a moral failing to not do anything it takes to get the results you need.").

The entire plot line is very dark as Peter's grief over his daughter takes him down a bad path. It is supposed to be (and was for me) uncomfortable to watch.