I think this quote pretty much sums up the position of anyone who thinks the New York Times was in the wrong.

The idea that we should give up freedoms listed in the Constitution in order to accomodate national security is pretty much the most horrible thing I can imagine. Why should a nation bother securing itself if it isn't free? Is the nation even worth protecting?

If national security was violated, then punish the Federal employee who broke confidentiality, don't punish the newspaper that repeated it. The newspaper has made no agreement to maintain confidentiality, and it should not be tried as though such an agreement were made.