This is an interesting topic. I pulled out Star Wars Insider Magazine, Issue #84, and took a look at the article about Clone Troopers on this one. This is what I came up with, to start:
Quote (p.31) - "Records salvaged from Kamino show that no genetic coding was used to implant obedience to this order (66). The efficiency with which this order was carried out was due to a genetic predisposition to be highly disciplined - and so to follow orders - that was developed and reinforced by rigorous training."
What remains in question, unfortunately, is *exactly* what kind of training Delta Squad recieved in terms of independent/creative thinking. The article above referred to Clone Troopers in general. We can still only speculate about the exact differences in the training of a standard Clone Trooper vs. a Commando. However, we can say that there are definite differences in the way a Special Forces soldier operates compared to a regular soldier, and many of those differences lie in the Special Force Commando's ability to respond more appropriately and more creatively to any challenging situation.
All this considered here is my *speculation* - Delta Squad was probably not even employed in Order 66. There were literally dozens of entire legions of Clone Troopers available for betrayal of their commanders. Seeing as how the Jedi were unsupecting, there would be no need for Commandos to perform these atrocities when unquestioning clones were available in hordes for completing the task.
Furthermore, the Commandos would indeed be more likely in general to question such an extreme order due to whatever training in independent thought they did recieve. This window of opprtunity, however small, would not appeal to Palpatine at all when considering the best way to implement Order 66. Imagine if a Commando Squad did actually rebel and refuse to slay a Jedi commander. Then you'd have a Clone Commando Squad being led by a Jedi against the Empire!!! That would be an insanely powerful group that could cause massive damage to the Empire at key vulnerable points, and would constitute *much* too large of a risk for Palpatine.
Finally, I'll share one more quote from Star Wars Insider Issue #84 in relation to this awesome topic before fianlly shutting up:
Quote (p.27) - "The highly independent Republic Commandos required almost no direction from Jedi command and were largely self-directing when given broad objectives. This greatly increased their 'clout per credit' by freeing up many Jedi for duty with the regular army."
Granted, Order 66 was not a "broad objective". It was very specific. But the dangers mentioned above combined with the independence training of a Commando in general lead me to think that they were not used in Order 66, and would be assigned the more broadly-based objectives of infiltration/stealth tasks that were more appropriate to their training, and less risky to the Empire.
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