It just seems the Jedi are fighting and refusing to ask any questions.
I don't know about that. I watched Episode III again earlier and the council's motives throughout were all about ending the war and forcing Palpatine to return his emergency powers to the senate. All the time the Jedi are fighting to end the war, but early on there was no clear picture as to who they were fighting. It was just droids attacking a planet so the republic fights back. I can't remember a republic offensive portrayed in the clone wars that was purely done to strike fear into the sepratists - all the attacks and battles the Jedi/Republic started were to achieve a specific goal, whether it was destroying Malevolence or stopping the droid factories on a fallen Geonosis.
It hasn't been until this season that the Jedi and Republic have started questioning the motives for the war, and this is most clearly displayed in Ahsoka's meeting with the teenage seppy she met while escorting Padme into separatist space. It gave her doubts about why they are fighting, and I think when the rest of the Jedi find themselves face to face with the people of the separatists, not just the droids they'll start to question it too.