Some principles can be applied to all situations, some can't. I suppose it's very much like the laws of physics. Newtonian laws are principles that are very effective at predicting the behavior of a certain class of object in a certain frame of reference. Once you start playing with the frame of reference, then you find that you need to ask Einstein so to speak.
Ethical principles can be said to work in the same way. Within a certain frame of reference, those ethics have to work at 100% otherwise there is room to call them into question. Most ethical trickery involves covertly shifting the frame of reference between propositions and trying to curve back to your choice of alternatives when meeting challenges. This is how many creationist fanatics try to create their so-called "paradoxes" that supposedly expose the "contradictions" of science.
The ethical frame of reference requires certain axiomatic assumptions about the nature of existence, just as a physical frame of reference requires axiomatic assumptions about the nature of physical reality. When we reach a contradiction it is a sign that either our perception is wrong, our reasoning is, or maybe it's one of those pesky axioms.
I think that if you make the ethical assumption that human life is the ultimate value and that that which is most important in preserving and sustaining it in a status suitable for the existence of human beings is what we should call good, then a valid chain of reasoning will lead you eventually to the conclusion that torture is universally bad.
The keystone is in the notion of human rights and the role they play in society. Rights cannot be applied to a group of people and then ignored in individual cases. They only function when applied universally.
Of course nobody should expect that a fully guilty man should have full rights. That is one of the reasons why we have tried to develop systems of justice that try to remove doubt from the process of assigning guilt. Because with the assignation of guilt for the violation of a human's rights comes a demand for the stripping of a certain degree of rights from the guilty party.
The problem with torture is it seems to go right to the heart of what we consider "justice", how it is best to determine guilt, and what extent that guilt necessitates a stripping of rights (i.e. how far do we strip someone's rights in response to a given crime).
I think one of the reasons that we have decided as a civilized culture not to strip all rights from the guilty is that the assignation of guilt is never as certain as we would necessarily like. And this is why Harris shifts the frame of reference in his argument to 100% certainty of 100% guilt, so as eliminate any room for sympathy. With this 100% certainty, he argues that it is 100% acceptable to torture a man under such conditions.
Initially in End of Faith he also posited that that certainty need not be 100% and that the fear of torturing people in error is equivalent to what our remorse should be in the tragic loss of life encompassed in the term "collateral damage." This would be a radical shift in frame of reference from the stance that guilt was unquestionable. However it appears that he has somewhat retreated from that rationale in his "Response to Controversy" posted on his site.
The challenge, as he puts it is this:
"unless one can produce an ethical argument against torturing Osama bin Laden, one does not have an argument against the use of torture in principle."
The demand for evidence is as crucial to ethics as the demand for evidence is crucial to the battle against the ignorance of creationism. We are innocent until proven guilty. This is a standard principle upon which most of secular legal theory is based. But it is not an axiom. Supporting it is a probabilistic assumption about the nature of crime and punishment which stands in direct opposition to the use of torture.
The assumption is that it is better to let a guilty man go free than to subject an innocent man to punishment. This is an assumption which acknowledges the reality of the process of discerning guilt from innocence, something which the rush to claims of perfect certainty tries to scuttle around. But what it also claims is that the preservation of certain key rights even for guilty men is more precious than concerns for security or retribution. If a murderer is acquitted, he may kill again. But it is better that he kill again than that an innocent man be executed.
A rational ethics must be based on a rational appreciation of the way the world really is. Unfortunately, the case that Harris builds up in his attack on religion, he undermines by his rush to create artificially contrived circumstances to justify what are very clearly actions that he thinks should be morally permissible.
Harris clearly assumes that the lives of many are somehow worth more than an individual life. What he fails to explain is that if it is ethical that an individual life can be sacrificed in the pursuit of war or justice or what have you, then what is there to prevent a greater group of people being sacrificed under the same conditions? Who makes the judgment as to which parties are 100% guilty? He claims that collateral damage is as ethical as torture, but is collateral damage ethical? Or is it more simply an unfortunate accident, something which an ethical party tries to minimize or avoid as much as possible?
I despise moral relativism just as Harris does. Al Qaeda is clearly guilty of horrible crimes. Bin Laden is clearly guilty of horrible crimes. But what quality is it that enables us to stand in judgment of them? It is the quality that we know that their behavior is atrocious, that they violate human rights, that they have no concept of justice themselves, and that they assault the values of life which are fundamental to a rational peace-loving society. It is because they have actively rejected civilization that they are uncivilized. But the only thing which allows us to look down on them is because we do respect life, we do have a concept of justice and we do honor human rights. But if that were to change, and were we to adopt the policies of our enemies, then we would relinquish that moral superiority. And, in a large way, they would have won.
Bin Laden is an evil man. But to torture him would be wrong, for the very reasons that it would be wrong to torture a murder convict. Rights must apply to all human beings equally. Rights are important because they must be defended for all people unilaterally else they have no meaning at all. As soon as we start deciding who gets rights and who doesn't we sacrifice the decision making procedure that makes us able to talk about rights in the first place.
In Abu Ghraib, I'm sure that the torture victims were all believed to be 100% guilty by their captors. But what we're learning is that they weren't necessarily so. In the real world, certainty is never 100%. We could pretend that it is, and adopt the code Napoleon as our new rational standard. But I think that the very concept of human rights would desolve in that atmosphere, just as it did at Abu Ghraib.
Of course once we accept that the focus of human rights is the individual in society and that all human beings possess those rights then we cannot justify torture even in just one case. If we need to make ethical provisions for every case, then what we are talking about is not a principle at all and it would of course be impossible to disprove something in principle which is purely situational.
I acknowledge that Harris has said that he perceives Abu Ghraib to be unethical. But I find it curious that he has not explained on what grounds he can hold that belief at the same time as the belief that torture is permissible.In order to read Harris' beliefs on the subject first-hand I recommend that you check out his book "The End of Faith" and his website here: http://www.samharris.org/site/full_text/response-to-controversy2/