If American troops have gratuitously beaten, tortured and murdered enemy soldiers they must be prosecuted. They have tarnished the military, besmirched their country, and violated the law of God. Such crimes cannot be allowed to go unpunished. Having said that, it must be asked why there is such a kerfuffle over alleged "desecration" of the Koran. It is not that we think it acceptable to treat this book disrespectfully, but distinctions need to be made.
Let's start with a question. What exactly is wrong with mistreating the Koran? Is the offense spiritual? Is it moral? Or is it merely political? Unless one believes that the Koran really is the word of God then it's hard to see how it could be spiritually offensive to treat it with contempt. Nor is it easy to see how flushing a book down a toilet (Has anyone asked whether this is even possible)could be immoral, even if it enrages the devout. After all, people are enraged by those who burn the flag and profanate the Bible, but that such acts are immoral seems a hard case to make in a secular society.
That leaves us with political offense. It is argued that it's wrong to mistreat the Koran because such behavior does not endear us to the world's Muslims, and, of course, here we agree. We should be sensitive to the religious sensibilities of those whose hearts we wish to win over, and our troops should for pragmatic reasons be ordered to treat the Koran in a reasonably dignified manner out of respect, not so much for the prisoners, who may indeed be detestable human beings, but for the multitudes of Muslims who are watching how we conduct ourselves. If soldiers violate this order they should be punished, but their punishment should be a consequence of defying an order. It should not be because their conduct is inherently despicable.
It will not do to reply that Muslims hold Christianity in contempt and therefore they have no claim on our respect. First, if we are Christians we are prima facie obligated to treat others with dignity, respect, and kindness. That means respecting, to the extent practicable, their most deeply held beliefs even if they don't respect ours. Second, it may be true that they do not respect Christian belief, but then they're not particularly eager to win our affections either. We are eager to win theirs. Without the support of the world's Muslims we'll never prevail in the war on terror, and we won't have that support if our troops don't display a modicum of deference to their most profound convictions.