I beleive Lucas intentionally contradicts the book universe just to prove to the authors that they have no power over his stories. He even commented that if you don't see it in the movie then it's not necessarly true.
For example, Lucas never intended Boba Fett to be such a huge character the the fans made him, and thus the book universe gave him grand background story. So, imo, just to spite the authors he gave Fett a different origin story... seems childish and goes to piss off a lot of people but meh. [/tangent]
The clone wars no doubt turned a lot of Jedi to the dark side, HOWEVER, I don't beleive that the Jedi of the "new" republic had the exact same ideals as those of the old republic. They were probably a lot more tolerant to their role as protectors, realizing their need to act as well as be mindful of the consequences of those actions.