I'm talking from the perspective of a non-Jedi. If I were in the order, I'd probably be less harsh: not only am I now part of the home team, but large chunks of what they do actually make sense once you see things from their perspective.
The problem is that they're secretive idiots who think they're above having to explain themselves to the rest of the galaxy, so it's not surprising that everyone else calls the war with Malak a Jedi Civil War. They both wave swords around, they both think they're above the law, and they both limit their interaction with the public to "I do what I want."
Sure, one's far more violent and openly avaricious than the other, but as Atton points out, the Jedi are just as willing to abandon their pacifism when it suits them (and only them). It just seems like such a poor system: the Jedi have to avoid prolonged conflict, as reality forces them to compromise their core beliefs. What is the point of a moral code that only works when no stress is placed on it?







