A good example of what I'm talking about (which involves doubts about the system and action taken by a Judge who questions it) is the recently-concluded IDW 12-issue Judge Dredd series that tells the story of "Mega City Zero".
As far as I am concerned nothing that happens in the IDW version of Dredd is canon in 2000AD Dredd.
Oh, I definitely agree as far as the Mega City Zero story (and "The Blessed Earth" sequel), as well as the first ongoing IDW series written by Duane Swierczynski (which seemed to me like a rehash of various plot threads from many previous-published Dredd stories). There is a Judge Dredd Year One miniseries by Matt Smith and Simon Coleby published by IDW that might have some claim to being canon, though. A Judge Dredd: Mega City Two and Judge Anderson miniseries were published that are set at specific 'blank' spots early in each character's career that don't seem like they conflict with any established canon stories, either. While at first I had a tendency to think anything first published outside of 2000 AD itself and the Megazine wouldn't be canon, there are those crossover stories with Batman, Aliens, Predator, etc. which are accepted and have also been printed within the pages of 2000 AD as well (not sure about where the Mars Attacks Judge Dredd series falls in that consideration, but the creators seem like they might be more 'authoritative' than people involved in the IDW ongoing comics).
Whether the story is canon or not isn't the point, though. It's merely an example of a type
of story, which deviates from the usual status quo because of a Judge (normally it would be Dredd) having philosophical doubts or questioning why things should be the way they are. I only brought it up because the details are recently fresh in my memory, and it represents a rather extreme
example. Yet there's nothing stopping any other Dredd story which seeks to examine the philosophical underpinnings or ethical values of the Judge system, or even of particular laws under that system, from leading to upsetting the status quo, either.