Originally Posted by James
I don't think the Clones are even capable of questioning the order. I always got the impression, as I mentioned in more detail in a previous post, that it's something ingrained into them. Like in their DNA, they don't even know it's there.
This got covered in the book "Dark Lord", the book taking place immediately following ROTS. It doesn't go into detail but some clones for sure were able to ignore their programming. The actually hid their Jedi companions and turned on Vader, who slaughtered them and the Jedi onc ehe found them.