The New York Times' stubborn use of honorifics—calling everyone by formal titles on second reference—is dumb. It's a goofy relic, and should be done away with. Done away with all at once. Not by withholding honorifics for people the editor doesn't like.
At Jill [Abramson] and Bill [Keller]'s request, we dropped the honorific for Bin Laden.
Without a "Mr." in front of his name, it was decided that we should capitalize the "B" in Bin Laden on second references.
So the paper's top editors realize the type of absurd situation that honorifics can produce—but instead of just eliminating them entirely, they selectively remove them. This is a form of editorializing. Which is something in which the NYT's news staff is not supposed to engage. Then again, the paper's editor-in-chief Bill Keller just wrote an opinion column endorsing a particular budget plan being proposed by a group of six particular Senators. "I'm rooting for the Gang of Six," writes the man who has the final word over the paper of record's ostensibly objective news pages.
The NYT is not even trying for that "objectivity" crap any more. You're so late to the party, guys!
UPDATE: NYT political reporter Nick Confessore says this on Twitter: "NYT stylebook: 'Omit courtesy titles with surnames of historic or pre-eminent figures no longer living: Curie; Hitler; Lenin; Napoleon.'" I did a quick check of the NYT obits for Ronald Reagan, Boris Yeltsin, and Saddam Hussein—all of them use honorifics. This part of the stylebook is clearly followed only at "Jill and Bill's" special direction.