The phrase "the Jedi treated the clones very well" sounds disturbingly similar to "slaveholders treated their slaves very well", both of which ignore the operative point, that they are slaves. Until the end of the wars, the clones could not leave the service, and we saw only a few managed to escape the service of the Empire and live independent lives (Rex, Gregor, and Wolffe as an example); but only once they were considered no longer useful to the Empire. The Jedi's participation in this institution does not leave them blameless. Additionally, the reason the Jedi fought to hold the Republic together was ultimately to maintain the central power of Coruscant, not because the Separatist were inherently evil (while that argument can be made). Windu's conversation with Palpatine confirms this in ATOC. The Jedi might not have been evil, but they were participants in a long litany of wider evils, which they did little to disavow themselves of. By the end of the TCW series, we see that Yoda himself is coming to this conclusion.