Originally Posted by James
It's funny because I'm not sure they've ever clarified, but I always thought Order 66 was something the Clones couldn't disobey. Like it was one of a long list of special orders implanted in their brains during their creation, just like an automatic robotic response. Perhaps afterward they would be like "What have I done?!" but at the time their eyes glaze over and they just follow the order.
Unless of course the Clone in question was defective in that manner, or part of a batch that was made before the order-implants were installed. In any case I've never felt like they had any real choice in the matter, to the point where the Clones weren't aware those orders even existed inside them until the word is given. This reasoning always made a lot more sense to me than soldiers who've fought side by side with the Jedi for years, in some cases even forming friendships, suddenly and unquestionably opening fire just because Palpatine told them too. One would also imagine, during all that time, at least one Clone would have made mention of Order 66 to a Jedi if the Clones were aware of it.
The way the film presents the execution of Order 66 made it seem that way initially, but it's part of a longer list of order for the clones to carry out.
This one specifically deals with the Jedi and using lethal force if they attempt to overthrow the Republic, which is how Palpatine played it out when he went in front of the Senate to show what the Jedi "did" to him.
Jedi probably knew of the order, but they wouldn't find reason for it to be initiated because of their alignment.