Im not 100% sure, but Id say...
Killing civilians acting in support roles as collateral damage
Targeting civilians acting in support roles
Killing civilians as collateral damage
and under some circumstances...
Targeting civilians to terrorize and/or demoralize
That last option sounds like what the 911 terrorists did. Does that mean they just did the same thing we would do?
I vote options 2,3 and 4.
This is what I was afraid of... people are mixing the idea of when one can start a war justly and what one can justly do in a war that one is already engaging in. The whole idea is that once a war has started, the acceptable range of behaviors broadens immensely, but this should only inform our conservatism in judging when it is just to start a war in the first place...
911 was wrong primarily because bin Laden had no just cause to go to war against America in the first place. The fact that he targeted civilians only adds to the atrocity, but the second part is admittedly debatable, as you point out. Many combatants have targeted civilians historically, including this country during WW2... but we were clearly attacked. The main reason 911 was an atrocity however was that bin Laden started the war himself and he had no just cause to start it to begin with.