You're mistaken in thinking the question of what the United States should do about the Guantanamo detainees is merely a "positive," "pragmatic" one that can safely avoid questions of theory. But don't feel alone in this—it's a mistake that most defenders of the administration's policy on the issue are making, too. They're saying it's self-evident that the detainees are not due even the initial protections granted POWs by the Geneva Convention, and you're saying that you can't fathom the opposite. In general, when two parties look at such an isolated set of facts and come up with diametrical conclusions—that, in addition, seem obvious—it's a good bet that theoretical differences, not factual ones, are at work.
And you (and many other administration folks and members of the punditocracy) are making it seem as if the Geneva Convention itself includes all you'd ever need to settle the detainees issue. And that's wrong, too. Here are a couple of for-instances: 1) All the talk about whether or not the detainees are "unlawful combatants" implies that the Geneva Convention defines this term. It does not. 2) The key passage in the Geneva Convention about "militias," the category it employs that comes closest to fitting a terrorist group, says they qualify for the protections it extends to POWs only if they conduct their operations "in accordance with the laws and customs of war." But unfortunately, the Geneva Convention doesn't define or specify what those are. 3) One of the benefits the Geneva Convention extends to POWs is the right to repatriation without delay "after the cessation of active hostilities." But do those captured in Afghanistan have to wait until anti-terror operations are over in the Philippines? The Geneva Convention doesn't contain even a hint of an answer.
And we need some theory here to avoid handling the detainees a certain way just because we want to or because we can. This is what's wrong with the pro-administration line, expressed most forcefully by that Charles Krauthammer column you cite, that POWs are protected by the Geneva Convention from substantive interrogation, but the United States needs all the information from terrorists it can get. A similar "argument" could be made for torture over Miranda rights or for theft over honest labor. So I think we're just plain stuck doing a bit of theorizing about what to do with the detainees.
And in my theory, the privileges and protections of the rules of war should extend to all and only those who avoid intentionally targeting noncombatants. (One last exegetical observation: You are wrong in saying that all four modern Geneva Conventions only "mention" protecting noncombatants—in each of them, noncombatants are the firstspecific example given of who is being protected.) And I arrive at this for pretty much the same reason you attribute to Dunant in his drafting of the first Geneva Convention: Even in war, it makes no moral sense to harm those who cannot harm you.
I should add that when you suggest that the sole alternative to granting the detainees POW status is to "starve them, poke their eyes out, torture them for the sheer vengeful joy of it …" you are misreading me. I stated previously and reaffirm here that in my view even those who don't play by the rules of war and therefore don't reap their benefits are entitled to humane treatment. But such treatment doesn't entail protection against interrogation or the right to return home. (And for the record, even if it were a violation of the Geneva Convention, I'd support interrogating the detainees because they probably know lots about in-the-works terrorist plots, and I'd support holding on to them because all past history indicates that if released, they will strike again.)
Many of the main consequences of my the-rules-only-cover-those-who-don't-target-noncombatants position would please the Bush administration because it would entitle the United States to: 1) substantively interrogate (most of) the Guantanamo detainees; 2) hold on to (most of) them even after the last shot is fired, whenever that is; 3) And handle (most of) their cases before special tribunals that don't fully conform to the judicial provisions of the Geneva Convention. But it would also avoid the grave sin the administration is currently at least appearing to commit, that of saying our handling of the detainees isn't governed by principle. It is—and I've supplied the principle. And it addresses your legitimate worry that we are, with our current handling of the detainees, telling the rest of the world that all bets are off about, e.g., snatching more Daniel Pearls or treating our soldiers badly when they're captured, because my principle explicitly punishes such snatches and protects lawful soldiering.
My approach also has another virtue the administration line manifestly lacks. The administration's insistence that what distinguishes lawful soldiers from terrorists is wearing a distinctive insignia and carrying weapons openly runs into the serious problem that, in Afghanistan at least, some U.S. special ops forces and anti-Taliban forces failed this acid test. They didn't, as far as we know, fail mine.