[T]he fact that somebody leaked this program causes great harm to the United States.
As a matter of pure logic, this assertion makes no sense. The only way that this disclosure could harm national security would be if it tipped off a terrorist under surveillance to the fact that his communications were being monitored. However, before the disclosure of this program, any terrorist would know based on public information that the federal government had the power to secretly obtain a warrant under FISA and monitor his phone calls and emails without his knowledge. (See the EFF's summary of the government's secret wiretapping power under FISA here). Thus any terrorist talking on the phone or engaging in email communications would have to know, even if he was an American citizen in the United States, that the government may have obtained a secret FISA warrant against him and could be monitoring his actual communications.
The disclosure of the NSA's secret wiretapping program therefore changes nothing in terms of a terrorist's knowledge, and simply could not under any circumstances "tip off" a terrorist that he was under surveillance. Accordingly, there are simply no circumstances under which disclosure of the program could harm national security. (Of course, if the disclosure were to then go on and identify actual persons under surveillance, then of course that could harm national security -- but clearly that is not what happened here).
Which leads us back to the question of why the NYT held off on publishing the NSA story for over a year. The NYT had an accurate story of undeniable national importance, the disclosure of which simply could not under any circumstances harm national security. So why on earth did it refuse to publish? Did it simply take Bush's assertion that disclosure would harm national security at face value, without engaging in the most simple analysis to demonstrate that it would not?
This is a big mystery that needs to be resolved. Unfortunately, the editors at the NYT are not talking:
I e-mailed a list of 28 questions to Bill Keller, the executive editor, on Dec. 19, three days after the article appeared. He promptly declined to respond to them. I then sent the same questions to Arthur Sulzberger Jr., the publisher, who also declined to respond. They held out no hope for a fuller explanation in the future.
It looks like, once again, reporting will need to be done on the reporting institution itself in order to get to the truth. I personally plan to keep an eye on The New York Observer, which had great coverage of the Judith Miller imbroglio within the halls of the Times. Hopefully they'll be similarly aggressive with this matter as well.