It sounds like the clerics could care less about the Newsweek semi-retraction. Although, to be fair, the cleric who made the threat is located in a "mountainous, conservative province near the borders of Tajikistan and China." It's certainly possible the Newsweek retraction hadn't reached him yet.
But it's also possible the U.S. got word of the threatened holy war via Internet chatter and pressured the government official who was the Newsweek source to change his story.
Even so, the story hasn't changed much. It's gone from the source saying he saw it in a military report to him saying he didn't know if he saw it in a military report or some other kind of report. What kind of retraction is that? In review, Newsweek today says:
Two weeks ago, in our issue dated May 9, Michael Isikoff and John Barry reported in a brief item in our Periscope section that U.S. military investigators had found evidence that American guards at the detention center in Guantanamo Bay, Cuba, had committed infractions in trying to get terror suspects to talk, including in one case flushing a Qur'an down a toilet. Their information came from a knowledgeable U.S. government source, and before deciding whether to publish it we approached two separate Defense Department officials for comment. One declined to give us a response; the other challenged another aspect of the story but did not dispute the Qur'an charge.
....Although other major news organizations had aired charges of Qur'an desecration based only on the testimony of detainees, we believed our story was newsworthy because a U.S. official said government investigators turned up this evidence. So we published the item.
....Last Friday, a top Pentagon spokesman told us....the Pentagon had investigated other desecration charges by detainees and found them "not credible." Our original source later said he couldn't be certain about reading of the alleged Qur'an incident in the report we cited, and said it might have been in other investigative documents or drafts.
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