Clones would understand what an order is, of course they would. They're trained. There is an executive order. Clones follow orders. Once it was authenticated as coming from the Chancellor, that's it. The lower clones obey the commander. The commander would only issue an order from a superior. Throughout the series we even see Jedi issue orders to commanders who pass it on to the men. At the Jedi Temple on Coruscant, you can clearly see when Bail meets them, it is not a trance. They are carrying out a mission to kill the Jedi at the Temple. QED! PRECISELY!!! Well said. The clones behaved better than stormtroopers purely because of ethical Jedi Generals. When they're gone, clones will be ruthless and follow their new superiors.