The publication of the article [on John McCain] capped three months of intense internal deliberations at the Times over whether to publish the negative piece and its most explosive charge about the affair. It pitted the reporters investigating the story, who believed they had nailed it, against executive editor Bill Keller, who believed they hadn’t. It likely cost the paper one investigative reporter, who decided to leave in frustration. And the Times ended up publishing a piece in which the institutional tensions about just what the story should be are palpable.
Lots of detail at the linked article.