But I don't see a "repudiation" of the story in their ombudsman's column. I did read these paragraphs, which don't amount to a repudiation at all:
But in the absence of a smoking gun, I asked Keller why he decided to run what he had.
“If the point of the story was to allege that McCain had an affair with a lobbyist, we’d have owed readers more compelling evidence than the conviction of senior staff members,” he replied. “But that was not the point of the story. The point of the story was that he behaved in such a way that his close aides felt the relationship constituted reckless behavior and feared it would ruin his career.”
I'm not sure it amounts to "repudiation" to correct a public misperception over what the story said.