Geof, I am not persuaded by your analysis of the use of presumptions to resolve the tension (whcih you acknowledge) between civil liberties and national security. You start off promisingly by stating that "Logic, for example, suggests that in dealing with conflicts between the national security and civil liberties judges should start with a healthy dose of deference to military and executive officials. This seems sensible for several reasons." And you list the reasons, such as that the judges don't know much about national security and the cost of invalidating a national-security measure can be catastrophic. If this is right, then necessarily the false positives will greatly outnumber the false negatives. Suppose judges always upheld national security measures, that is, made the presumption irrebuttable. Then there would never be a false negative; that is, there would never be a case in which the court would prevent the government from responding effectively to a real danger. The only judicial mistakes would be false positives--allowing the government to respond to dangers that turned out to be nonexistent (or to respond disproportionately to slight dangers). If judges should hesitate to meddle in national security, as I believe they should (including for the reasons you give), then it is right that false positives should preponderate over false negatives, perhaps greatly. I don't, by the way, think that the presumption should be irrebuttable; for as I said, I agree with the result in Hamdi. (In the case of ordinary crimes, where the danger to the nation is much less than in the case of national security, the system reverses the presumption--false positives, namely convicting the innocent--are weighted more heavily than false negatives--failing to convict the guilty.)
You say that history shows that the courts have been too timid in checking national-security measures. History merely shows, consistent with the presumption in favor of upholding national-security measures, that the courts err on the side of permission. If courts were as aggressive as you seem to want them to be, we would never have violated civil liberties, but instead lost several wars. I know that Santayana said that those who forget history are condemned to repeat it. But there is also the quip about the Bourbon kings--that they learned nothing and forgot nothing. I do think the United States faces a unique threat in the intersection between the extremism that is coursing through the vast Islamic world (1.3 billion people) and the growing lethality and availability (to nonstate actors) of conventional and unconventional weaponry. I think that courts should tie the hands of the executive branch and Congress in responding to this threat only when the presumption in favor of upholding national-security measures against legal challenges is compellingly rebutted, which I think it was in the Hamdi case.
Are you serious in suggesting that the presumption should be reversed, and a heavy burden placed on the government of justifying to courts the necessity of national-security measures? I doubt that you mean this literally. I hope you don't.
I also think that the courts have contributed, albeit inadvertenly, to some of our national security problems, perhaps including the 9/11 attacks. They have accepted the presumption against judicial medddling in national security, but have not (perhaps could not) try to limit the application to national security of constitutional provisions invoked in routine civil and criminal litigation. The Fourth Amendment exclusionary rule made the Justice Department hesitant to conduct searches (for example of Moussaoui's laptop) and to demand information from the CIA that might compromise prosecutions. The exclusionary rule may also have contributed to the too-narrow scope of FISA. Extravagant judicial interpretations of freedom of speech create reluctance on the part of law enforcement and intelligence authorities to conduct surveillance of extremist preachers and speakers. Judicially created rules about the scope of the right to a public trial and about the right of a criminal defendant to represent himself make criminal prosecutions of terrorists likely to backfire--the government is forced to reveal information that assists terrorists to evade detection and to allow the defendant to turn the trial into a political circus. Yet I don't think the courts are a very serious impediment to effective national-security intelligence. I think we can have an effective system, including a domestic intelligrence agency separate from the FBI, within the framework of existing constitutional law certainly, and probably statutory law as well though FISA may (or may not) be illegal. This conclusion reflects my belief, which I have tried to document in Uncertain Shield, that there are effective alternatives to the criminal-justice system for dealing with terrorist threats.