From this article in the Washington Post, we can conclude that, in the mind of the New York Times, the risk that banks might “stop cooperating” with a program of proven effectiveness was trumped by the assertions of “uncomfortable” officials. And this decision was reached despite there being no clear evidence that the program was illegal.

Keller said he spent more than an hour in late May listening to Treasury Secretary John Snow argue against publication of the story. He said that he also got a call from Negroponte, the national intelligence czar, and that three former officials also made the case to Times editors: Tom Kean and Lee Hamilton, chairmen of the 9/11 commission, and Democratic Rep. John Murtha of Pennsylvania—an outspoken critic of the war in Iraq.

The main argument they made to me, extensively and at length, besides that the program is valuable and legitimate, was that there are a lot of banks that are very sensitive to public opinion, and if this sees the light of day, they may stop cooperating,” Keller said.

He acknowledged, as did the Times article, that there was no clear evidence that the banking program was illegal. But, he said, “there were officials who talked to us who were uncomfortable with the legality of this program, and others who were uncomfortable with the sense that what started as a temporary program had acquired a kind of permanence.”