[quote=OutlawedPanda]
I have one issue, though... The Clone Troopers would not be guarding the Jedi during the execution of Order 66. Order 66 is a contingency protocol for the clones in case the Jedi go rogue. The clones are designed not to fight it and would immediately turn hostile on the Jedi.
[/quote]

There were a few Clone Troopers who disobeyed the order.

I think [url=http://starwars.wikia.com/wiki/Omega_Squad]Omega Squad[/url] disobeyed the Order and would later disband.

Another Clone Trooper, [url=http://starwars.wikia.com/wiki/Ordo_Skirata]Ordo[/url] disobeyed the order and fled to Mandalore.

EDIT: And I think Delta Squad (from a Star Wars video) also dismissed the order, although they later joined the 501st who hunted down more Jedi.

Iron Team also protected their Jedi, and proceeded to fight off the other Clones who tried to kill them.