Good news, bad news
Good news! Guantanamo Bay interrogators might not have defiled the Koran. Newsweek's evidence for this claim turns out to be sketchy. If the Koran was never flushed down the toilet, then the truth surpasses even my dejected hope that the Koran flushing was an isolated incident that the government was already dealing with responsibly.
The bad news, of course, is that the rumor is already out. Riots have happened, people have died. Given the absence of trust for the United States in much of the Muslim world, the rumor may continue to have a life of its own, just as the rumors about pig and cow oil did a century and a half ago when India did not trust Britain.
The other bad news is that all sorts of other "inappropriate interrogation tactics" are more than rumors. Terrible things have happened, some of which were an affront to the detainees' religion (like that bizarre one about the fake menstruation blood). I don't want to get into the futile task of debating how the desecration of the Holy Book compares to other "interrogation tactics" in its wrongness, but it does appear to have a particularly strong power to move people.
Speaking personally, it always sucks when a story that gets to you turns out to be an unsubstantiated rumor.
Here's a brief history of the story:
A "senior U.S. government official" told Newsweek reporter Michael Isikoff that a draft of a report by the U.S. Southern Command in Miami mentioned cases of Koran flushing. Newsweek mentioned this claim in one sentence of an article. Before publishing the article, they vetted it with "a senior Pentagon official" who did not comment on that claim. Several days after the Newsweek article was published, it was translated into Arabic. Although rumors of Koran flushing had been around before, this report from a credible source sparked a variety of troubling incidents, including riots in Afghanistan which led to deaths. Since the riots, the Pentagon has denied the charge of Koran defiling and then the original source has indicated that he may have misremembered where he read about the allegations of Koran desecration. Newsweek has apologized.