While I agree that everything does not need an explanation, I think the clones sundenly turning to "Empire mode" deserves one. The order 66 is all what Lucas found because he lost so much screen time in the 2 previous movies that he rushed the third movie. So I think keeping order 66 (or some sort of signal that would turn instantly all troops to "Empire mode") would be the lesser of two evil because we just can't have the clones fithing along with the Jedi for years sundenly turning against them only because Palp says so, IMO.