Frankly considering the history of the Warcraft universe, war and and atrocities are more common than not.
The Night Elves committed plenty of atrocities against the trolls as an example.
The issue is in WOW how do you frame war and atrocities in a way that both sides still come off looking "good" or at least "noble".
If they had just stuck to pure red vs blue territorial conquest type PVP goals then much of this would be a moot point.
But PVP in the game has always been an afterthought so they had to come up with grander visions for faction conflict beyond PVP.
Hence you get the stories we got since Cataclysm, which almost always start with someone on the Horde side doing something stupid(Garrosh).
Or someone on the Alliance side thinking that the Horde did something stupid even though they didnt (broken shore).
Unfortunately none of that is quite compelling story wise. They should just leave it at the factions skirmish over resources but aren't "good" or "evil" inherently. Or if they do want to be "edgy" then just have someone be evil for whatever reason and be done with it. There is no reason that folks cant be corrupted anymore by "evil" forces or just have pure selfish interests. And part of the problem of not having the Legion around is that they were always the convenient go to for "evil" lurking around every corner. Similar with the old gods. Heck if they really wanted to be edgy they could have gone with that sword sticking out of Azeroth being corrupted and promoting evil actions among both factions........