If my Brother was killed, I would take out retribution on their brother and leave it at that; that is retribution. I DO NOT have the right to kill their brother in addition; that would be an act of aggression. Bringing the analogy back to 9/11, we slapped around the man who killed our brother, left him bleeding, and started beating the crap out of his second cousin.
I'm afraid wars are not great respecters of the rights of individuals on both sides. That goes double for a war that is started by the killing of 3000 American civilians, whose rights were abruptly truncated on 9/11. Since we were not a part of the governments in those countries, there were limits to our knowledge about the ultimate sponsors and to our ability to get at them.
Some might say that Hirohito should have been our primary target in WWII. But the reality is that he had an entire country's military protecting him. And ultimately securing victory at a reasonable cost in American lives required the dropping of two atomic bombs. Was it fair to either Japanese civilians or the Japanese draftees who were forced to join the Imperial Japanese military that we had to kill them to get at Hirohito? No. But that's war for you. A lot of bystanders have to get killed before the decision makers will back off.
I think it might also be timely to point out that 9/11 occurred *before* and was the cause of the invasions of Afghanistan and Iraq. Whatever grievances bin Laden had in mind prior to 9/11, they certainly did not include those invasions. Interestingly enough, al Qaeda has slaughtered *fewer* American civilians after the invasion of Afghanistan and Iraq than before.