Blame them? I would cheer them on. Bunch of hypocritical, egotistical people who only care about their own little cult and its splinter group and have forgotten to do what they say they're all about finally get taken down a peg or eight? Rock on, Palps, you slimy chakaar!
EDIT: Alright, some of the Jedi weren't that bad, but still, most of them were as rotton as they come. Some (Etain, Bardan) were truly trying to help people who couldn't help themselves, but the majority were blinded by their own self-importance.
as much as I dislike the entire Jedi Order, I don't know if I'd say they deserved it? and certainly most of them weren't blinded by self-importance, since the population of Jedi versus how many we actually know of don't really match up :p but if the Jedi Council do, arrange, and order terrible things (which they had), that doesn't mean their lower ranks should also be sentenced to death, particularly when many of those who participated in the war (and ultimately killed at 66) were children/child soldiers
in order for the clones to have been able to harbor dissent towards the Jedi, in order for them to have been able to "think for themselves," they HAD to have been exposed to normal civilian life--which we know isn't the case, particularly for infantry. in keeping a grand army under control, the clones needed to be separated from the concept of being free people, or needed to be kept separated from empathizing with it... in effect, the structure of the GCA kept the clones isolated from the rest of the Republic so they would not then become their own people. sure, they formed bonds and communities, but because it was all strictly interconnected, it kept them even more isolated and insular. there's no way the clones could have been able to then break that mold and think for themselves, and then add what dred said and it's a miracle any
clones were able to disobey the order at all.