Agreed. It makes sense when you think about it. If you give clones free will, a lot of them wouldn't have gone through with Order 66. Having the knowledge repressed in the clones minds also makes sense as it prevents the knowledge from slipping out or a friendly clone warning the Jedi about it.
I was hoping that Rex would have refused the Order 66 command but this episodes pretty much confirms he won't be able to.
Interesting bit...the Jar Jar two-parter was written by Jonathan Rinzler, who is currently adapting The Star Wars series for Dark Horse and has done all those Making of Star Wars books.