stormtrooper commander

To an extent, something similar to your head canon happened in star wars canon and EU, but on a smaller scale. If I was in a position like Dave Filoni's where I was working on a show like Rebels or something, and in my little fantasy world, if I had you on my team, I would try to compromise your interesting head canon idea to fit in with both canon and legends. 
Basically there would have been a few clone battallions who did what you said-they didn't execute order 66 (which in some areas was the story in canon/legends) and some of those clones eventually deserted or joined the rebellion. We see Rex helping out Ghost Crew in rebels, and we hear about the Kamino Uprising in Star Wars Battle Front 2. 
There are some comics/novels where some planets felt like the Galactic Empire protected them from the clone wars. This was before the prequels and hasn't officially been retconned, but asides from the CIS dabbling in making clone soldiers of some types of aliens, and the Kamino Uprising, there could be something where a batch of clones went haywire and was a menace to the public until they got "saved" by the Empire. Perhaps there could be a false/black flag conspiracy story about how Palpatine would send some brainwashed clones to massacre a planet that was reluctant to join the empire, and when said batch of rogue clones had "softened up" said planet, the Empire would rush into "liberate" said planet that was desperate for a savior and now more open to submitting to Imperial rule out of need of security and gratitude. (also have the idea that the empire would sometimes use leftover battle droids to attack a planet that wasn't ready to join the empire to make them desperate to join it quicker. Even if it refused to submit, the droid attacks would soften it up. It would explain what the empire did to some of the leftover droids, and how it used the whole problem/reaction/solution on a smaller scale after the clone wars to get planets to join it while still looking like the hero when it captured said planet. Also, it could blame said attacks on the rebels or something). 
Likewise, my idea is that the empire could send a few bad clones, ones dressed up like your good clones, to do a false flag attack on the people of a planet or village so they would think your good rebel clones were attacking them, and then join the empire to wipe out said loyalist republic clones. 
Not only would it make people see the rebels and loyalist clones as terrorists, and make said people cling to the empire for safety, but it could push Palpatine's agenda of either weaning the Imperial Military off of clone troopers and/or severely limiting the use of clone troopers to Imperial Military, made to have no loyalty to the Old Republic. This would be regardless of whether we go with Disney Canon that said that the empire immediately stopped cloning right after the clone wars, or EU Legends that says there was a more gradual phasing out of Fett clone dependency by cloning other people until their recruitment/conscription quotas of regular birth born humans was filled. Occasionally, the empire would make batches of "flash clones" by a different company, but they were shorter lived and lower quality (but then again, the empire was about quantity over quality after the first death star blew up, and nobody would know cuz the clones wore the same outfits and were diverse from different people, only Vader's Fist being all or mostly Fett Clones). 
Palpatine would do this to not only wean himself off of complete Fett Clone dependency (since clones could apparently be hijacked and were vulnerable to being wiped out quicker by a virus, as well as having less independent thinking skills, and were generally expensive, and had to grow up 10 years before combat) but would also appeal to the human supremacists who looked down on clones as not quite human. 
In my little head canon fantasy, your designs for both clone and human troopers would come in. The designs you draw would be regular human storm troopers who had extra training to specialize in taking down Fett Clone troopers. Perhaps they would use weapons that spread diseases and viruses mean't to target the Fett DNA strand and ignore everyone else, who knows. 
I just like being creative and thinking out loud