I read this post (
http://attanagra.livejournal.com/8862.html). I knew full well Traviss was no fan of the Jedi; having read all of her EU books it's about as obvious as a mushroom cloud. But I hadn't known she disliked them THAT much or about her rather unfair black-and-white assessment of anyone who would stick up for the Jedi.
I am totally against human cloning and creating an army of meat puppets to be a society's set of cannon fodder is morally unconscionable. While it's shameful the Jedi Council never gave that issue any thought, I don't think it justifies slaughtering the entire Order, from infants and cleaning ladies on up.
The Dark Side has grown strong by the time of the prequel era and in AOTC, Yoda and Mace Windu discuss how it has affected their ability to use the Force. One could argue that it also completely messed with their judgment. Not to say there's no moral culpability; I'm just saying the Jedi, clouded by the Dark Side and carried along by rapidly-changing events, made some really bad decisions ranging from how they handled Anakin to joining the Clone Wars to shrugging off any moral issues of using people bred for battle.
Still, I also have to question what would have happened had the Jedi simply refused to fight for the Republic or made some kind of objection to using clone warriors. Could the Senate or Palpatine order them to do it anyway? If they still refused, what would have happened then? And consider public opinion…what would they think if their own tribe of superheroes decide to get all hippie on them as they're being attacked? Remember that the Republic had no military at the time the Clone Wars started. The Separatist threat was here and now; there was no time to recruit and train a massive army overnight (though there was a non-Jedi officer corps in the CW cartoon). So, in the midst of this crisis, the Jedi were doing what they had to do to protect the Republic, knowing there really wasn't a way to back out. The Jedi were new to the war business; they appreciated having the help of trained soldiers. Moreover, the Jedi knew from the get-go that the Sith were behind the Separatist movement…they knew the Sith had to be stopped (though they didn’t know the degree of the Sith's involvement). Yes, they cashed in their values but from their standpoint, there really wasn't a good decision vs. a bad decision. They didn't have the whole picture. So they made what they thought was the least-worst decision.
In any case, the Jedi were stuck right where Sidious wanted them, in the middle of his evil trap. It was Sidious and Dooku who had the clone army created in the first place. They were willing to sacrifice gazillions of lives--Separatists, Jedi, clones, civilians, etc..--just to knock out the Order and seize control of the Republic. Did the Emperor really care about the clones any more than the Jedi did? Nope. At least the Jedi gave their guys names. The stormtroopers are just numbered. Vader is the only one who seems to have any regard for them whatsoever. Otherwise, they're expected to be target practice for the Rebels.
The Jedi were not evil. The Council were, like almost every character in the prequel trilogy, Palpatine's useful idiots.