Free Drones.
Everybody calls them anarchists. Their symbol is the anarchist symbol, and yet they only seem to preach that the protectorate is bad, not that any kind of government is bad. If you talk to them, they all seem like at least decent people; they're very friendly and caring. Contrast that with the protectorate, who range from stern to psychopathic, and for the non-military ones from depressed to just-happy-to-have-a-safe-job. Some of the bad things they are known for sure sound like the doing of the CAU (like gassing the train that doctor arrived on) for false flag purposes. The game has to go out of it's way to make them sound bad: anarchist symbols, the train quest, the envoy quest, the bad rail crossing ending.
If you remove Malek, the CAU, and whichever types gave Holloway his intel (and that's just what we know of from the protectorate side; the free drones and gorsky have even worse things to say), then you'd have a decently good argument for the protectorate. As it stands, they're a straight up bad-guy empire, and that's coming from someone who thinks the nazis were the good guys in real life. Another thing to think about is this: if the free drones can organize to fight the protectorate, then they could handle the iron heads instead if there were no protectorate, no big military needed.
Final word: I'd rather deal with raiders than a big empire military lead by psychopaths.