Ahh... it's been ages since I contributed to a debate node. Game on!
I personally find the above example to not be a fair comparison against the September 11 attacks. The key is that, should someone walk up to you and punch you, you know two very important things - who did it (the pugilist) and where s/he is (right in front of you). And that leaves the protester (myself, since I'm still tentatively against the recent attacks on Afghanistan, pending further details) with two options.
The first is you can punch the offender. This fits in perfectly with the belief that innocents should not be punished, since it's pretty clear who's guilty of what, right? Just make sure you can swing a fist around without accidentally smacking a bystander in the face.
But, hopefully, you wouldn't need to do that... I mean, his family might come after you, thinking you started the fight, or that he was just being playful as a kitten, or whatever. Hopefully, there'll be police around. And the attacker could then simply and effectively be brought to justice. That's part of the point of having a justice system, you know - in theory and usually in practice, the justice system is how you avoid a circle of violence. Bring in an impartial judge, set up laws that are inviolate for all parties involved. Guarantee a high level of fairness. Determine fault and sentence accordingly and evenhandedly. Sure, sometimes the system is unfair, and sometimes (especially depending on the chosen judgement) the violence will continue anyways, but it's the best idea out there. Take this high-voltage circuit of violence and short it into the ground. That's justice for you..
Very rarely do you find someone who doesn't think that the people behind the terrorist attacks should be brought before a fair trial. Usually the complaints will be, in order, that we don't know exactly who did this to us, we don't know where we can find these people, and the trial will be grossly unfair... but if those problems can be solved (and they can be, with enough worldwide scrutiny and deliberate pacing), then it's on, brother.
Quick aside - yes, Virginia, there are those who would consider the attackers to be innocent, only reacting to what ills the United States have perpetrated on them. To those apologists, I proclaim 'poppycock'. Yes, the United States has made many moves of questionable (at best) morals, and we need to answer for them. But a terrorist attack is still a terrorist attack. Justice For All.
So, in closing, I'd like to bring up the the following scenario, to see if it fits the situation at hand more closely...
You're out, walking around (as everyone does in this hypothetical Town X), when suddenly, a sniper opens fire. Fifteen, sixteen dead, everyone frightened out of their wits. It doesn't take long to see that the shots came from the direction of a group of buildings where a few nutters with guns live. One of the nutters is particularly famous for making weekly threats about killing the townspeople... but he's friends with the asshole landlords who run the building, and they won't let anyone in to have a word with this guy (who denies any wrongdoing, but enjoys the bloodbath immensely). And this guy's got some of the tenants on his side, too. So... what do you do? Destroy the buildings, and punish everyone living in them, regardless of what they've done? Swoop in and try and capture the guy, and have to contend with the asshole landlords and the tenants who like him? They ain't gonna give him up, no matter what evidence you bring, you know. What if someone who likes this guy decides to grab a rifle and try their luck at popping pedestrians? Now, there's a good amount of circumstantial evidence that this guy's the one, but what if it's all just... circumstantial? Townspeople are out for blood, and they might not agree with this 'insufficient evidence' ruling. You can clear off the streets, force people to stay in their homes and live like rats, but that doesn't change the fact that there's a guy out there with a gun. Maybe you could do nothing, claim that 'non-violence is the best answer'. So the gunman gets bored and starts shooting again, and you've solved nothing except maybe your annoying neighbor got whacked this time around. So what do you do?
Here's one thing you can do. You can beware of simple solutions to complex problems.