This is really very simple and I'm not going to explain it more than once.
Despite our desire for revenge and justice and despite all the arguments of both the Bush and Obama administrations, there is only one way to look at the cases of Khalid Sheikh Mohammed and his confederates who are on their way to New York to face trial.
Despite all the whining and posturing from international do-gooder organizations, it is indisputable fact that non-uniformed irregular combatants and terrorists and terrorist conspirators and organizers are absolutely not regular soldiers and are by no means protected by the Geneva Convention. Despite the attempts to shoehorn them into a new category of "illegal enemy combatants," they should not be tried in military tribunals, a form of trial normally reserved only for internal military discipline, though it was used for war crimes and for spies in World War II.
The truth is that once you accept that they are not soldiers under the Geneva Convention, to try them under a military tribunal is to assign them a status which they have not earned and do not deserve. You effectively elevate them and their cause to a level of legitimacy reserved for agents of a sovereign state. Since they clearly did not act on behalf of such a state it makes no sense to give them that status.
Historically, groups who declared ideological war on the United States and carried out acts of terror, but did not do it on behalf of any foreign nation, like the Symbionese Liberation Army, have been treated as criminal conspiracies under the law. That is the precedent which ought to apply here. Patty Hearst, H. Rap Brown, Tim McVeigh, and President Obama's friends Bill Ayers and Bernardine Dohrn didn't face military tribunals and didn't get sent to GITMO. They went to a regular court and a regular jail after being tried for their crimes as common criminals.
Before anyone complains that this is different because these attackers came from outside the United States, the truth is that we routinely prosecute criminals who are not United States citizens, including the hundreds of thousands of illegal aliens who committed crimes and are now in our jails, and high-profile mass murderers like the late and unlamented serial killer Angel Maturino Reséndiz, who was executed in Texas despite the efforts of the Mexican government to have him repatriated.
The reality is that there's very little reason not to try terrorists in regular United States courts, beyond the convenience of the prosecutors, concern for public sentiment, and a belief that military trials will be quicker and more likely to convict on weak evidence. Other arguments of convenience are also questionable. The ideology of the criminal, his violent inclinations, what role he may play in inspiring others, or the possibility of reprisals all have no standing at all in the legal process. None of these is a legitimate reason to override the basic right to a trial by jury to which criminals are entitled under our constitution, under common law, and as a matter of basic human rights.
Sentiment and the desire for revenge should never be allowed to override fact when it comes to the law. The fact that these terrorists were not soldiers, did not act on behalf of any nation, and are functionally no different from any other common murderer or group of murderous conspirators is undeniable. Since they are criminals they should be tried as criminals in both the state and federal courts and be punished under the laws of those jurisdictions. In this case, that would mean a trip to Indiana where federal executions are carried out by lethal injection.