WOW what a good episode, one of the best yet from the entire series! I was on the edge of my seat most of the way through it.
I'm pretty sure this is a spoiler thread but I'm gunna put a Spoiler Warning here anyway!
So Krell had turned to the dark side and I'm glad them went this way if not only to justify his characterization. Looking back on this past arc Krell has been like a heel in wrestling, getting us all riled up with his actions and speaking of wrestling I literally shouted oww!! when Krell did that back breaker on a clone, my girlfriend looked at me gone out and we got to see more of the Krell lightsaber action I was wanting.
When they had the two clones lined up for the execution and you saw the blasters fired, I thought 'wow, I cant believe they actually did it' and was relieved when the next shot showed they had purposely missed.
I was pleased with the ending but there is a small part of me that wishes Krell had escaped so we could have seen him in future episodes, and it would have been nice to see the clones report to Anakin, Kenobi and the Council just to see their reactions to Krell's turn.
After watching this episode I now think markatisu is right and this arc has partially been about setting up that some Clones will overpower their genetic programming and not follow Order 66 (though I still think it will be very few in terms of numbers) some lines in this epsidoe really drill that home, such as:
"Some clones are just defective, they aren't able to succumb to authority."
"We are loyal soldiers, we follow orders, but we are not a bunch of unthinking droids. We are men! We must be trusted to make the right decisions, especially when the orders we are given are wrong."
I don't think Order 66 erases or changes any of the clones personality or memories and turns them into slaves though (if I've interpreted you correctly gbagok). The clones are loyal to The Republic and Palpatine not the Jedi, and this episode show just that. IMO all Order 66 does is trigger a command saying all Jedi are now enemies of The Republic and are to be killed. I don't think the clones are even aware of the command before its issued, it's just something that has been programmed into there subconscious or genetic make up and Palpatine is probably the only person who can issue it.
I'm going to watch all four of these episodes again back-to-back this afternoon.
I think this episode had a lot of good messages for children today, about conformity, standing up for your self, questioning authority and not following it blindly.