I'm off travelling for a few days, but I wanted to point to this Kevin Drum post, asking whether it's legitimate to kill 18 innocent civilians if that's the only way to get four bad guys.
I think anyone's answer to that now-academic question may be less important than the implications.* If you disagree with Kevin and say "no" it's not legitimate, then you're a near-pacifist - modern warfare has these kinds of ratios all the time, and it would be hard to fight without them. You'd probably have disavow anything short of dangerous, on-the-ground , visual contact-type of military activity.
If you say "yes", then it works both ways. The Pentagon was a military target, not a civilian target, and the civilians who died on the plane crashing into it were just acceptable collateral damage. Of course one could still object that the attack was an unjustified act of war, but not that it was a war crime because it killed civilians.
*Of course, it may not seem academic to the relatives of the people killed.