That game includes a mission of the player joining Anakin in assaulting the Jedi Temple and massacring the Jedi there (no younglings, though). The narration for that mission shows that the clones acted out of loyalty, rather than some forced programming. “We all knew what was about to happen, what we were about to do,” the narration says. “Did we have any doubts? Any private traitorous thoughts? Perhaps, but no one said a word.”
This is what makes the two approaches different. Having the clones be conflicted adds to Lucas’ vision of the prequels as a story about the rise of a fascist state with devoted fanatics. The clones, no matter how good they seemed, ended up betraying their friends and comrades because they followed orders. “The Clone Wars” tried to retain some of that by having the inhibitor chip also trigger a code phrase in the clones as they carried on Order 66 — “Good soldiers follow orders.” By making them docile programmed slaves, however, the franchise takes a tamer approach. Granted, given the young demographic of the show and how liked the clones were, avoiding making them cold killers makes sense.
As Filoni said, there was another point to the inhibitor chip in addition to simply explaining where Order 66 came from: “It was also about showing that not everything that Palpatine did was flawless, that there were near misses, that there were opportunities to stop it.” That is the ultimate thesis of the prequels, particularly “The Clone Wars.” Everything could have been avoided if only someone had done a few things differently. If only Obi-Wan had taken Count Dooku’s warning seriously in “Attack of the Clones.” Or if Shaak Ti had listened to Fives. Maybe it could have all been avoided.