The truth is that OBL/AQ actively targeted innocent civilians. Western forces in Iraq and Afghanistan did not go out with the intention of killing innocent civilians but sometimes thses things are unavoidable, either due to mistakes/miscommunication or down to the fact that bombs cannot differentiate between Taliban and civilians or other NATO forces for that matter.
As true as this may be, it really doesn't matter. People fight with the means that they have at their disposal. It's easy to claim the high ground when you have orders of magnitudes more money to spend on the military and advanced technology, but the reality is that there are many people in the world who perceive themselves as victims of US foreign policy (and many of them really are victims of US foreign economic policy), and they fight back with whatever means they have available.
Perhaps a playground example is in order. Let's say a clique of huge guys bully somebody who is all by himself, and this person tries to defend himself by kicking one of them in the nuts. After that, the huge guys claim that that's no fair, they would never intentionally kick somebody in the nuts, and use that as justification for further bullying. Yes, they're right, kicking somebody in the nuts is not nice. Then again, they are so much superior in their sheer force that they can afford not to use all the tools at their disposal. So requiring the little guy to refrain from kicking them in the nuts to defend himself simply isn't fair on some level.
This doesn't mean that I want to live in a world where people kick each other in the nuts. I'd much prefer a world where nobody does that. But the only way to get there is for both the huge and the small guys to agree to abide by the rules of some higher authority. In the playground case, that would be teachers, parents, or in the extreme, police et al. In the case of US vs. Terrorists, this would be some truly neutral (or should I say Lawful Neutral) international court of justice.
And the truth - as much as hearing this probably hurts the USians here - is that in all such situation, the big guy needs to be the one who backs down first. (How I wish right now that all those self-proclaimed Christians in the US would actually insist on US foreign policy following Christian values...)
So yeah, bin Laden got what he deserved (though it sickens me to see all those pictures of celebrations in the US - come on guys! You are just as bad as the flag burners in the middle east), but the whole "innocent civilians" angle does not give the US the the moral high ground here, even if it were completely true.