[Treasury Department Assistant Secretary for Public Affairs Tony] Fratto says he believed "[The NY Times] had about 80% of the story, but they had about 30% of it wrong." So the Administration decided that, in the interest of telling a more complete and accurate story, they would declassify a series of talking points about the program. They discussed those with the Times the next day, June 22. [emphasis mine]
If this leak was so damaging to national security, why did the administration go to the trouble of correcting the Times? Wouldn't an incorrect story throw the terrorists off balance? Obviously the answer to both of these questions is no. The story goes on to say that the Treasury Department knew for a week that the Times had this information for two months so they definitely had a game plan for when this came out.
The Treasury Department then leaked the same information the Times had to the WSJ and the LA Times because in the Journal's editor's opinion, "that Treasury also felt Mr. Simpson would write a straighter story than the Times, which was pushing a violation-of-privacy angle; on our reading of the two June 23 stories, he did." Surprising they would think that, isn't.
The bottom line is that if the administration really wanted to keep as much information secret as possible about SWIFT, they wouldn't have corrected the NY Times, and if they were truly interested in punishing the NY Times they could have let them print the story as is and then gave the WSJ the corrected facts leaving the Times with egg on it's face. In the real world, that's a much bigger punishment to a newspaper than a ridiculous Congressional condemnation. But that wasn't the case, they simply wanted to use the Times to feed the base.