As has been mentioned by others above, the Times also needed to slow down renewal of the Patriot Act. But obviously, publishing this Risen series was a big gamble. They initially gained some negative traction against the Administration because persons in Congress and the media, I believe, were cued to the release of the first story. But now the public seems to be taking the side of Bush and national security. I think the Iraqi elections and Bush's rising poll numbers was definitely a factor here.
Your speculation makes sense for me. And like you note, I think the Times and the rest of the left is now is a pickle, since the public seems to agree with the Bush administration that it's okay to intercept al-Queada communications coming into this country.
(I can't imagine how anyone could have a problem with that, but that's why I'm not a liberal. And conversely, I guess that liberals must be baffled by those of us who want to treat al-Queada as a greater threat than the Bush administration.)
I'll be interested to see if liberals keep this NSA story alive -- part of them wants to keep it alive, even though another part of them has got to know it makes them look bad and makes the administration look good.