i think the clones knew of order 66 before it was given. they knew instantly what it meant when sidious said to excecute it. they are completly loyal to the rebublic so they wouldnt question it, especially if they heard about it before hand. id say the emperor made them all aware of the possibility of jedi rebellion and told them that as soon as he gives the word to kill them. they are grown to have no independance and trained not to question orders so i dont think much thought came into it. and becuase of the lack of anger and malace the jedi probably wouldnt pick up on it very easily, which is shown especially when aayla secura was killed, she sensed something, saw the troopers raise their weapons and she reached for her saber and turned around to see what they were aiming at, only to be shot in the back by them. i think it wouldnt have taken plo koon a while to realise what was going on too, when they started shooting at him he probably thought he missed some enemy fighter that was on his back before he realised he was the target. the jedi on the speeder didnt even look at the troopers when the nodded to eachother and dropped back behind her. i think the commandos could have disobeyed though. they have alot more independance than the standard trooper. the arc's might have questioned it too, but the standard trooper will obey without question.