Jonah, I couldn’t agree more with your point (and related article) about the unexamined issue of damage done to the civilian justice system by bringing our terrorist enemies into it. In Willful Blindness, which was just republished in paperback with a new preface, I talk about this very issue:

There is a profound but often undetected corrosion of our justice system when we force the square peg of terrorism into its round hole. My belief that we oughtn’t treat terrorists as criminals, far from being caused by disdain for the rigorous demands of civilian due process, reflects instead an abiding reverence for our system’s majesty. Treating jihadists as if they were U.S. citizens accused of crimes and presumed innocent reduces the quality of justice Americans receive from their courts.
Islamic militants are significantly different both in make-up and goals from run-of-the-mill citizens and immigrants accused of crimes. They are not in it for the money. They desire neither to beat nor cheat the system, but rather to subvert and overthrow it. They are not just about getting an edge in the here and now—their aspirations, however grandiose they may seem to us, are universalist and eternal, such that pursuit of those ends is, for most jihadists, more vital than living to see them attained. They are a formidable foe, and, as noted above, the national security imperatives they present are simply absent from the overwhelming run of criminal cases.
As a result, when we bring them into our criminal justice system, we have to cut corners—and hope that no one, least of all ourselves, will discern that along with the corners we are cutting important principles. Innocence is not so readily presumed when juries, often having been screened for their attitudes about the death penalty, see intense courtroom security around palpably incarcerated defendants and other endangered trial participants. The legally required showing of probable cause for a search warrant is apt to be loosely construed when agents, prosecutors, and judges know denial of the warrant may mean a massive bombing plot is allowed to proceed. Sensitive intelligence that is relevant and potentially helpful to the defense—the kind of probative information that would unquestionably be disclosed in a normal criminal case—may be redacted, diluted, or outright denied to a terrorist’s counsel, for to disseminate it, especially in wartime, is to educate the enemy at the cost of civilian and military lives.
Since we obdurately declare we are according alleged terrorists the same quality of justice that we would give to the alleged tax cheat, we necessarily cannot carry all of this off without ratcheting down justice for the tax cheat—and everyone else accused of crime. Civilian justice is a zero-sum arrangement. Principles and precedents we create in terrorism cases generally get applied across the board. This, ineluctably, effects a diminution in the rights and remedies of the vast majority of defendants—for the most part, American citizens who, in our system, are liberally afforded those benefits precisely because we presume them innocent. It sounds ennobling to say we treat terrorists just like we treat everyone else, but if we really are doing that, everyone else is necessarily being treated worse. That is not the system we aspire to.
Worse still, this state of affairs incongruously redounds to the benefit of the terrorist. Initially, this is because his central aim is to undermine our system, so in a very concrete way he succeeds whenever justice is diminished. Later, as government countermeasures come to appear more oppressive, it is because civil society comes increasingly to blame the government rather than the terrorists. In fact, the terrorists—the lightening rod for all of this—come perversely to be portrayed, and to some extent perceived, as symbols of embattled liberal principles, the very ones it is their utopian mission to eradicate. The ill-informed and sometimes malignant campaigns against the Patriot Act and the National Security Agency’s terrorist surveillance program are examples of this phenomenon.
In sum, trials in the criminal justice system don’t work for terrorism. They work for terrorists.