Its easy to say "this was wrong" but there is a pretty stark absence of what alternative measures they should have taken. Palpatine set things up to pretty harshly compel them to take these specific paths, so its not like they had a lot of choice about the things they did, especially involving the Clones. They knew something was up, but given the whole "enemy government led by someone trying to destroy us, specifically" thing going on, its not like they can just put the clones away until they know more about them. The CIS rolling over the Republic due to their lack of an army isnt the victory Palpatine expected, but he would sure take it if the Jedi gave it to him.