I have a few thoughts, which may or may not be self-contradictory or even coherent, but here goes.
I try to stick to a grunt's-eye view. The protagonist isn't saving the world per-se, just his skin & his buddies. Even in an atrocious cause, that can still be a laudable goal. A reader can understand a human goal.
He may have been cheesy, but look what Sven Hassel did for German troops on the eastern front (entertaining as hell, btw). His characters were guys who just want to survive a terrible situation, rather than fanatics trying to conquer Europe for Hitler.
My protagonists may be on a mission, even an overarching goal, but I like to contrast the purity of their vision with the messy reality around them.
Part of the problem with a story like the one referenced is that the conflict is not really over. For Greeks and Turks, 1453 is still a hot topic. Presenting one side's heroic vision is bound to piss-off the other.
Before 2007, I'd have insisted no one could get worked up over the Greco-Persian wars. Was I wrong. Zach Snyder and Frank Miller pushed buttons that should have been rusted in place.
And here's the thing, I didn't even find it that entertaining. It's one thing to watch a fantasy chock full of Peckinpah homages and fascist aesthetics as abs-of-steel-warriors slaughter Tolkein trolls and club kids. But the battle of Thermopylae is a TRUE story of heroism. What draws me to it is the courage of the REAL men who stayed and fought, knowing they would die. Instead I was trying to figure out why King Xerxes was a 10-foot tall gay, robot from outer space.
It's sort of the opposite of what Tolkein argued for in "The Critics and the Monster." He agreed Beowulf's setting is rooted in some poorly-remembered historical facts. But the story only references them to heighten the fantasy. A true story of Ingjald, Hrothulf, and Hrothgar would simply be another sordid tale of greed and revenge. By fighting a monster, Beowulf moves away from that. His heroism is pure, because it is mythic. It is not juvenile, but liberating.
The corollary seems to me, that when dealing with history, the story-teller needs the gritty, messy stuff of truth. And I don't mean you can't fudge a date, or a setting, or edit a character or two. I mean the truth that in a violent, amoral world, you don't always get to have all the good guys on your side. In fact your side may not be very good at all from the other side's (or even your own!) perspective. Even when fighting vile wretches, they may be courageous, or pathetic, or not very bad, or snappy dressers, or have some redeeming quality (I'm sure there's always a few scumbags who just need killing, but they are a minority, and by no means confined to the other side).
As much as I like a bad-guy to really commit to being bad, once an author goes to the wide focus, cast-of-thousands approach, no matter how despicable an evil overlord is, most of his grunts are just ordinary schmucks doing a dirty job. Unless they are orcs, in which case it's fantasy.
I think there's another issue to consider: focus. Critics often seem to want the part to stand for the whole. Just because most of the shmucks just want to do their dirty job and go home, it doesn't mean there aren't some fellows who really enjoy it. They may make for a more interesting story simply because they are more motivated (sure I could have gone on leave, but there are so many suspects to torture, this is my busy season, but I like it, I'm a people person). Sick bastards can be lots of fun (Sven Hassel loved 'em).
But, no matter how well-documented your sick bastard is, someone may well claim you are maligning the good intentions of whatever ethnic/political/religious group they came from. "Why is the torturer an Endursky? Endurskies don't torture people. I'm an Endursky and I never tortured anyone..." Now torture by Endursky security forces may be well-documented, an Endursky torturer may be what the plot calls for, but if someone has an axe to grind...
