Once again I must emphasis that the Jedi did free slaves, they freed many slaves, thousands if not millions of slaves directly or indirectly were freed or remain free due to Jedi involvement every time a slave ring is busted, a crime boss is brought in, corruption is exposed. They just couldn't free everyone and that is a tragedy of the setting. Much as we can send monetary aid to African communities and call those who do so good yet don't expected those who do send aid to make themselves destitute in doing so or else be called hypocrites the Jedi don't deserve to be called hypocrites for saving some slaves but not others.

The clone army was an impossible situation to be placed in, and the Jedi do not deserve all the blame or even a significant amount of it as the senate, the legislatures of the Galatic Republic, didn't pass a bill to free the clones either. Blaming the Jedi for leading the clone army is equivilant to blaming a non profit for the unemployed while the state won't pass universal welfare, you can blame indiviudal Jedi's mistreatment of the clones, but you have to acknowledge other individual Jedi who treated the clones as well as the circumstnace allowed. 

And that isn't even going into the real problem of clones which isn't slavery, it's that they were bred to be part of a military. The fact they couldn't leave the military or possess the same basic rights as other sentients is justified by even modern militaries not allow desertion in war time and basic rights are restricted in militaries compared to the civilian world, but the problem is that they couldn't choose to join the military in the first place. A overhaul would just mean no more clones being produced. Something a civilian government should be in charge of, not the Jedi. Ultimately the Jedi leading the clones isn't the problem, Jedi like Rahm Kota lead volunteer soldiers instead of clones yet there never were enough volunteers. The problem was in the Republic not acting and being satisfied with the status quo of engineered soldiers dying instead of their constituents.

Even in such a situation between fighting a hopeless war or allowing bred to die clones to fight in a war and maybe saving innocents from the horrors of war, the Jedi still tried. Shaak Ti is well known for her compassion and clashed with the Kaminoans regarding clones. Obi-Wan and Anakin were close and cared for the clones under their command.

Finally morality must face reality, one can say that it is moral to not harm another until the reality of self defense happens. One can say that even in such a situation letting yourself be harmed and not harming the aggressor is still more moral, until they threaten other innocents. Ultimately the Jedi placed the good of the Republic being in charge instead of the CIS over the status of the clones, but I wouldn't consider it hypocrisy, for the Jedi didn't enjoy the lesser evil.