I'm going to go out on a limb here and say that this reminds me of the books I've read on the American Civil War. The North and the South have their justifications for going to war against each other, and their reasons are so convincing that although I agree with the North more I know that the South is not entirely wrong and the North is not entirely right. Plus the people involved aren't all morally "good". The good generals are the ones who make terrible blunders (like the slaughter at Cold Harbor) and keep going on because they say the other army's lost men they can't replace and it kept their army occupied. People called General Grant a butcher and railed against General Sherman's "total war" and these men didn't flinch, kept moving on, kept doing what they had to do. In fact, General Sherman once professed that he hated war and that he brought total war to the people in order to end the war faster.
And the Rebel generals were quite honorable and the Rebel soldiers very honest, even if they were fighting for a cause that would've destroyed the United States of America. Talk about moral ambiguity.
So basically I'm just saying that I see the anti-hero as a morally ambiguous character. In more basically I'm just saying, "Look at Dr. House."