I've been playing BattleFront II the past few days, and the first half of the story campaign provides a unique perspective on this. The Clones (presumably all of them) were trained and ordered in a way that gave them impression that the Jedi weren't flawless, and could be fooled. The clones beleived that the Jedi were conspirators and were eventually going to mutiny. And no matter what the feelings or respect they had for their Jedi leaders, they knew all along that when the time came, they'd do the "right" thing and obey their orders.
God is a placebo with nasty side effects.