Back in the day and even nowadays, people had a problem with that you were playing as unsupervised and unrelgulated elite soldiers that didn't have to answer to anybody and that you were just shooting up innocent people.
And maybe it's because I'm a European, but I never understood why anybody would think that, because nothing in the game supports that idea. First of all, we can't kill any civilians, the game simply doesn't allow it.
And secondly, any enemy you see is inherently hostile. It doesn't matter if it are the Cleaners, the LMB, the Rikers, Hyenas, Outcasts, True Sons or local thugs, they all shoot at you without any provocation. There is no instance in the game were you can walk past them peacefully without getting attacked.
And it's also not a case of: "Oh, these guys are just missunderstood". No, we actively see thouse groups planting bombs, taking hostages, setting stuff on fire, killing unarmed civilians, laying ambushes and doing all kind of illegal stuff. Especially the Rikers do all kind of fucked up stuff to the remaining police force in the first game.
So no, I don't buy the notion that the Division agents are the bad guys and massacring civilians without repercussion, because we actually do improve the situation for the general population in both games, while everyone else just loots, murders and tortures everyone they see.