Well, the idea is that the Jedi are "bad" for
accepting the clone army.
However, just as we saw in TPM with slavery in Hutt space, the Jedi don't really have the authority to shut down Kamino, at least not by AOTC; that film tells us Kamino isn't in the Republic.
( Also, even if the Republic had rejected the army, the clones were trained for war and could still have ended up being used for their original purpose, but in some other conflict. )