To touch on the religion aspect, I don't think Scruffy was saying that the Jedi religion or organization was inherently evil, but that perhaps the Jedi order had become too stagnant, dogmatic, and militant by the time of the republic's fall (according to the PT at least). In other words, from a particular point of view you could really make them all sound very corrupt.

Though I will say that I don't believe George was purposely formulating that lesson to the detail that Scruffy describes. I think he had some basics ideas as he wrote out the story and sort of ended up with some basic lessons that work in accordance with his currently-adopted, anti-war, supposedly-Buddhist beliefs. Most of the particulars that Scuffy mentioned were therefore unintentional.