Let's deal with the second point first. Even if the riots really were provoked by nothing more than the Newsweek article, Newsweek can hardly be held responsible for the violent acts of others who happened to have read mistaken reports in their magazine. But in fact, there's every reason to believe that a murderous mob stirred up in response to a Newsweek article would have been happy to have been stirred up by just about any convenient pretext. Indeed, there's ample precedent for Islamist riots responding to completely false reports generated by untrustworthy sources. Often, these riots are carefully planned and prepared for reasons that have nothing to do with the ostensible provocation, and there are plausible claims that this one, too, falls into that category. Under the circumstances, Newsweek's role in causing these riots was most likely pretty minor.
As for the supposed horror of flushing a Koran down the toilet--well, all I can say is: if it had been a Bible flushed down the toilet, the Supreme Court would have stepped in by now to prevent the US government from objecting to it. Sure, US interrogators flushing a Koran down a toilet might offend some devout Muslims. But then, interrogating suspected terrorists no doubt offends some devout Muslims, as well. What matters is not whether violent Muslims in Afghanistan object to American interrogation techniques, but rather whether mistreating a Koran is within the bounds of American standards of interrogation--which, after all, includes some fairly harsh treatment of the interrogated prisoners themselves. And while it's hard for me to imagine Koran-flushing actually being a useful technique, neither do I see a compelling reason for excluding it on moral grounds, rioting Afghans notwithstanding.