Yeah, that's what the point about "a few mentally unhinged" people is. There have always existed a minority of people who are able to get into power and commit truly, outrageously heinous acts or isolated incidents of soliders going really off the rails. If like, there was this one powerful general who went around indulging in nonsense, maybe. But the problem in these stories that the vast, vast majority of the bad guys are some flavor of ridiculous evil shit that's divorced from rational thought or motivation. You can't have an entire government of fucked up people who are just fucked up. Sure, soldiers commit gangrapes or descended into self reinforcing spirals of war crimes and excuses. People power become sheltered from the blow back their actions might otherwise have. But even at worst, in real life, things are rarely as bad as some of the off hand villains in these stories. It goes beyond simple breakdown of moral and discipline or the shady predilections of those in power. There's reasons these things happen but also don't immediately result into everyone turning into lunatics. That's the problem. The story exists to have people do ridiculous, off the wall evil shit so that they can be reviled and destroyed.
No one is saying AGK needed to be this deep, reflective work on the nature of institutional evil and endemic depravity. But when it chooses these sorts of easy outs to facilitate wank, people are going to call that out and rightly so. It's not wrong for a manga to do these things, it's just that it's a specific narrative device to achieve a specific end and people aren't all on board with that. AGK is not in any way a realistic depiction of how fucked up real life can get. It's completely divorced from those things.