Phil, I find myself in the awkward position of disagreeing both with Scalia's comments about Boumediene and your critique of them .
You offer three reasons why Scalia's comments are wrong. Your first point, that we are really at war with "a very diverse constellation of [radical Islamist] groups" rather that "radical Islamists" generally, sounds correct to me. But I'm not sure why it is relevant to Scalia's argument. Scalia's shorthand may have been imprecise, but I don't see that as such a critical error to the extent it was one at all.
Your second point, that we might release fewer bad terrorists with court fact-findings than military ones, seems unlikely to me. Presumably the availability of habeas relief only expands the group of people that may be released; I'm not sure how it would limit it. And while the military may make mistakes in releasing people who are dangerous, I would imagine judges will make more. Judges don't have a lot of experience in figuring out which detainees are real terrorists and which aren't. The Constitution may require them to do it, but that doesn't mean they'll be good at it.
Your third point, that extending habeas jurisdiction to potential terrorists may lessen the threat the detainees pose by impressing them with our commitment to due process, also seems unlikely. The detainees have been held for six years, and any legal process will take a few more years; I doubt a detainee who gets out after a decade or so in Gitmo will think well of the United States for its judicial process.
To be clear, I'm not saying I agree with Justice Scalia's argument or the fact he made it. I don't. To begin with, I doubt Boumediene will have much practical effect. I predict it will prove to be a largely symbolic opinion, rather than one that will make a major difference in the real world.
Second, and more important, I think it's quite troublesome when Supreme Court justices devote large chunks of dissents (or worse yet, time in TV appearances) to decrying the practical impact of majority opinions. That only leaves the impression that the dissenting justice based his own vote on policy rather than law. I would rather judges apply the law as they see it and save the sound bites for the elected branches. But with that said, I'm not sure your post "crushed" Scalia's "canards" in quite the way you hoped.