So you believe Rex would gun down Ashoka, if she had been Anakins Padawan at the time of Order 66?
Which she isn't of course.
Remember Commanders, ARCs and Commandoes aren't genetically altered to be more obedient, and I say MORE there as a completely obedient soldier isn't worth much if they can't think creatively, which is what makes them better than droids.
My opinion is that clones that served alongside and formed bounds with Jedi and even non-clone individuals who weren't obviously an absolute liability would think twice about following such an out of the blue order. Many might follow along with less bounded clones taking the first shots but I'd have liked the more advanced clones to at least ask for confirmation or reasons before blindly following orders.
It makes me imagine the guys in the Nuke silos launching armageddon without any kind of confirmation, or situational brief.
Also what about the possibility of someone sending falso orders to the Clones if they follow them so blindly.
You bring up a very interesting point 50Stone. However, let's look at another well known clone. Commander Thire. First episode showed Thire and Yoda on a mission together forming lasting partnerships, however, Epidose 3 shows Thire in the Senate chamber looking for Yoday to kill him. Yes certain clones and clone commanders had the choice to follow Order 66 or not.
Let's look at another clone, Commander Cody. Cody has always been a comrade of Obi-Wan (anyone watching the Clone Wars series can see that). However, once good ol Palps sends the Order (personally), Cody switches to soldier mode and follows his general orders. He even says in the Novelization of Episode 3 "Why did that have to come after I gave him his lightsaber?"
There were clones that did not follow orders and asssited the Jedi in escape (reading Order 66 and the next book Imperial Commandos 501st, reveales that, as does the book, Dark Lord). However all clones are slo included in Order 66 and are branded traitors to the new Empire.
As for Ashoka, well, we don't know what happens to her. It's more than likely if she was killed during O66, she was probably killed by another clone commander and his clones.
The Battlefront 2 game that is about the 501st clones reveals also that the clones not only knew that Order 66 was gonna happen but some actually wished quick and painless deathes for their Jedi Commanders (they specifically refer to Aayla Secura and the clones wishing her a quick death once the order came down).
As for Order 66 being sent out... According to the Order itself it can only be sent out by the Chancellor. That's why Palps contacts the Specific Clone Commanders and Arcs himself. Only he can send out the order.
My only point was that the clones weren't so much programmed as they were trained and as such, they had a choice to follow the order or not.