Maybe it was supposed to tweak McCain into showing his temper. Maybe they thought if they threw the allegation out there it would somehow get legs. Maybe they just hoped there was some truth to it, even though they never uncovered any.
In any case, the fact is the NY Times ran a story about about an allegation of an inappropriate relationship between McCain and a young lobbyist without any evidence, based on anonymous "former aides" and put it on the front page. It's very telling that the notion that the NY Times published a completely bogus, politically motivated story isn't even considered improbable. They've done it before. The Times is no longer regarded as a source of objective, accurate information.
This incident just reinforces that notion. The story will turn from focussing on McCain to focussing on the behavior of the Times and its editors. The more they try to defend their indefensible methods and practices, the more they will be regarded as a partisan rag. It's a shame that an institution with such a long, rich history is transforming itself into the "National Enquirer" of daily newspapers. Maybe someday a white knight will come along, clean house and turn it into a legitimate news source again.