The more I watch the O66 scene, the more I become convinced that it was not a indescriminate command to all the clones to wipe out all the Jedi, but sent only to any ARCs and the Clone Commanders. Consider:
- Obi-Wan:
Cody receives the order, seems to only tell the AT-TE crew to open fire and then carry out a search. - Aayla:
Unless I'm mistaken, those troopers that kill her are all ARCs, with the exception of Commander Bly. I'm not too sure about this, though. - Stass Allie:
The Clone on the bike closest to the camera is her Commander, and we know that Clone helmets have built in comms, so it isn't nesercerry for the other trooper to be told about o66, only "drop back and open fire on my order" or something like that. - Yoda
Same deal as before, one of the clones that tried to kill him was the Commander of his forces. - Ki-Adi-Mundi
This is where it may fall apart, as I have no fucking clue what those guys in the funky red outfits were. - Plo Koon
This may be reaching abit, but the OS says that " the clone commander pilot opened fire", so that could be taken to mean that the pilot was a clone commander (and thus received O66) or just the commander of the ARC-170.
Anyway, from these examples it can be inferred that O66 was only sent to ARCs and the Commanders serving under the Jedi, instead of all the Clone being told that the Jedi were all to be killed on sight (Apart from the Clones at the temple, obviously.)
Why does this matter? Well, there's been a few discussions on the likelyhood of a Jedi surviving O66, and IIRC the general consensus was that it hinged on whether every Clone had been given an order to kill all Jedi, or whether it was just the higher-ranking Clones who were told.
Of course, I've probably made a massive mistake somewhere in there, so please correct me if I have.