In this case the Afghan people allowed the Taliban to rule and thus share some measure of the blame for 9/11. So they are not really "innocent".
So if the civilians of this country allowed Baby Bush to become president and someone doesn't like the bad things that Baby Bush did, civilian casualties in this country would be ok?
It always amazes me that the most extreme people have absolutely no ability to put themselves in the other guy's shoes.
Yes. If not then it is far to easy for government leaders to shelter themselves.
Lets presume our enemies have a legitimate reason for attacking us (I'm not saying they do/did). Then, as long as their targets are our government and/or military, and they do not seek civilian casualties, such collateral damage is just a part of how the world really works.
For example, if they'd only attacked the Pentagon on 9/11, and as a result some civilian janitors got killed, that would be acceptable and not criminal. By attacking the WTC however, where the targets were specifically civilians, the act was criminal.