"It's also important to note that war crimes happen in every war - and that the way to judge a society is how it handles such things."
Follow the logic here: since war crimes are an inevitable part of war, the way to judge a society is on how it treats war crimes when it chooses to go to war.
I think to reach this conclusion over the inevitability of war crimes is insane (or, if you prefer, highlights intrinsic acceptance of militarism). To me, the inevitability of war crimes in war calls into question the effectiveness and morality of warfare, and suggests the way to judge a society might be how much of its resources it devotes to warfare, the efforts it takes to avoid war, and how and why it chooses to go to war. To a pacifist, Sullivan's statement is a bit like saying that if you let your kids throw rocks at passing cars, they'll inevitably hit a few pedestrians, but what matters is that you tell them to avoid hitting pedestrians, and punish them if they do.
But if you accept (or support) warfare, and you accept that warfare inevitably leads to war crimes, you're left with the conclusion that what matters is how the society treats the inevitable war crimes. When you've accepted a culture of militarism, you don't reach the conclusion that war itself is the problem.