Originally Posted by Kurgan
Of course. But the EU provides "wiggle room" for those who want to believe in "heroic clones who would never do such a thing" by saying they weren't all programmed to be completely loyal.
Thus they can have their Republic Commandos and ARC Troopers sitting on Kamino drinking coffee, without the vaguest inkling of what their brothers are up to.
Go figure... :P
There's actually a short story (comic) called "Orders" from Ryan Kaufman about some Republic Commandos who indeed receive Order 66 and do what they have to - they kill their Jedi General ... One of them explains to a kid that they have nothing except each other and their orders (sometimes good, sometimes bad) which they have to follow.
So there are
not only the "ordinary" troops, but also Commandos (and probably some ARCs, too) who obey orders without question and kill the Jedi.