This was seemingly the case in at least 2 or so stories and the Battlefront II storyline before Disney. When some clone squads (specifically those who had served and survived under one jedi general from start to finish) received word of Order 66, they were fully aware of what the 150 orders were, but members of each squad came to their own conclusion; one squad believed this must be an error or a CIS sabotage, while another squad believed the order they were reluctant to believe that their jedi commander was a traitor and was probably ignorant of "what the Jedi order had done". So both squads tried to save their commanders but ended up paying the ultimate price for their insubordination, as the more obedient and younger troopers among them killed their brothers. If I remember right, only 5 or 6 jedi were actually saved by their troopers, while the other few survivors only made it out by killing their troopers, hiding from them or by not taking part in the war at the time. Their primary cause for their defiance was that they viewed their commanders as the closest things they had to parental figures, with their commanders treating them like padawans or family. The Battlefront II storyline had the usually cold and uncaring main trooper show some regret over having to kill Aayla Secura, hoping that he could make her death as quick as possible to spare her from any suffering.
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As such, I don't think a chip would even have been necessary since the Kamino education facility was their entire lives before they were shipped onto the battlefield. Its all they ever knew so of course they would gladly obey and believe everything it was given to them (not to mention they lack the age and experience to know better). Everything they learned there was hotwired into them by the strictest education and brainwashing methods, not just to betray the jedi but genetically engineered and indoctrinated for max loyalty and believing that all orders are for the best. Some orders not only included killing the jedi, but some involved killing all senators, the chancellor, and even suicide. It was a twisted yet believable scenario, and as we saw and read in much SW media the Kaminoans were cold and fucked up like that. With mentions and stories of Kaminoans "taking away" young clones who couldn't follow orders or score high enough points in tests for "re-education" only to never be seen again, either to be experimented on, turned into slave labor or sold for cheap. Kaminoans would even eliminate their own children over the slightest "defect" like unusual eye colors. Emotional Kaminoans were rare as fuck, and only a very small few ever actually held anything akin to fondness for their clone "children". Anyway, its quite clear that even in Filoni Wars this brain chip thing was a last minute decision since the Umbara Arc clearly showed otherwise near the end. And the ROTS video game shows Kenobi using Mind Tricks to help the clones "fight their programming", but even that could be taken as him believing they've been brainwashed since he himself is probably ignorant of why they've become hostile. Although chances are that Order 66 might've functioned as some sort of brainwashing trigger.
