I remember this, too, and it's the second part I take issue with. A judgment call of "likely enough true" when the reality is "entirely fictional" points, in my opinion, to either a lack of judgment, or a lack of journalistic ethics. As others have pointed out, very basic fact-checking was all that was needed to figure out this guy was a complete fraud.
We should not be praising the New York Times for letting its standards slip because the story was so cool, then eventually - years later! - realizing they'd let them slip a little too much and half-heartedly apologizing.