The Clone Troopers were absolutely, unswervingly loyal to the Republic. They could not be bribed, they could not be dissuaded or disillusioned to combat. They served the Republic, and the Republic decided to grant Chancellor Palpatine more and more authority over the use of his army.
Battle Droids have a program. A scenario. If the tide of battle turns in a way outside of the battle plan, the Droid is essentially useless (ex. blowing up a command station).
Order 66, like every other battle order they were "programmed" with during their training on Kamino, was a legitamate scenario that they were trained to deal with on the battlefield. The Clones didn't obey orders blindly, like robots, they obeyed orders to secure victory. Without question.
One second, Commander Cody and General Kenobi and battlefield comrades. Order 66 is decreed on a secure channel from the Chancellor's Office, and Cody blasts that Jedi traitor right off the cliff face. There was no malice or hatred in their minds. There was no "darkness" to have been detected by the Jedi. They are following a legal decree from the Chancellor. They are following orders.
The clones who disobeyed were largely ARC Troopers, trained to work extremely close to their Jedi commanders, and their affinity for their comrades superceded the validity of Order 66 in their minds... and they were dealt with harshly for their independent thinking to disobey a direct order.
No droid army, no matter how numerous or advanced could ever be used to eradicate the Jedi. The Jedi are too resourceful, and the Jedi Reflex could detect the mechanical movements a split second before it happens.
The Clones are living beings with an imprint within the Force... if something is awry, the Jedi would easily be able to sense it, right? Go ask a dead Jedi.
"Organic"... all the way, baby.
"Reality is a nice place to visit... but I wouldn't want to live there."