Of course. “Do I see Lieutenant Calley? Do I see Captain Medina? Do I see Gen’ral Kostner and all his crew?” I’m old enough to have had at least a nascent political awareness when those things happened, to say nothing of Abu Ghraib. (The first that I really became aware that politicians were … human … came when I saw my congressman throw a punch right at a Chicago cop on national television on the floor of the 1968 Democratic convention.)
But note that the atrocities happened at relatively low levels - the orders may have originated from on high, but the atrocities were not committed by an organized action of a large military unit, but by relatively few individual platoon and company commanders and the soldiers under their command. In the case of Sơn Mỹ, the soldiers who tried to stop it were denounced as traitors at the time, but eventually decorated for heroism in saving unarmed non-combatants.
In the nightmare scenario, you likely will see individual platoons, companies, maybe even battalions entering the fray on one side or another. The indoctrination that the military don’t step into American politics runs deep enough in the officer corps, though, that you’re extremely unlikely to see a whole regiment or division fighting as a unit. And the uncertainty over who’s really in charge and the confusion over conflicting orders would greatly hamper their effectiveness. Either the chain of command will be intact, and the military will be staying out of domestic politics, or else they will be fighting as an extremely well-armed but disorganized rabble.