It was _clear from the beginning_ (especially due to the non-existence of the well organized Left in the States) that the U.S. government would invade one or more nations in the Middle East, making the 9/11 bombings a pretext for war, rather than criminal justice. So, it seems to me that the subject line "Is there a nonviolent response to September 11?" is missing the point, especially now that the war actually began, making extradition & other questions of criminal justice moot. There of course remain the question of international laws which the U.S. invasion violates, but no one expects any American to be brought to justice for any war crime committed in this war.
Could there have been a non-violent alternative to the war? Theoretically, yes, but practically, no, as the U.S. government's aim was not to put the perpetrators (the most responsible of whom died in the bombings anyhow) on trial but to reassert its military might (restoring confidence in its competence which was shaken by the Pentagon bombing), reaffirm its political leadership, expand its sphere of influence (e.g., more US military bases in the Middle East & Central Asia), and install a more useful regime than the present one in Afghanistan.
Yoshie