|A serial killer or zombie?|
If Order 66 had to be a biological program, I'd at least have liked something more along those lines. Make the Clone Troopers conscious of their actions but also irresistibly compelled to kill Jedi. That way Fives' struggle would still have meaning because the clones could then try to resist Order 66, even if most of them would have failed. Morally they'd still be interesting characters. Because of this, the execution of Order 66 would still have its tragic meaning because it would still be a betrayal. However, given the clones' programming, we'd also still be permitted to feel some sympathy for the clones' plight even as we abhor their actions.
I suspect producer Dave Filoni and scriptwriter Katie Lucas decided on the "zombie" route because it does absolve the clones of responsibility. The Clone Wars is a kids' show and there are many kids who buy Clone Trooper costumes, toys, etc. For some kids, the Clone Troopers are the heroes of the story, not the villains. It probably would have been quite traumatic if these kids realized they were idolizing the moral equivalent of the Wehrmacht. In terms of responsibility to their primary audience, The Clone Wars team probably made the right call, even if it makes for poorer art.