The fact is that people at the CIA asked Mrs. Wilson to talk to Mr. Wilson about going to Niger to investigate the Yellowcake claims is a part of the story that seems to be getting no play.
The reason why Novak wrote about this was because Wilson rebuked the Yellowcake evidence put forward by British intelligence and repeated in the now-famous "16 words" in the SOTU address.
She is a crux of why he went their to begin with and his . She is an integral part of the story. So, when Novak revealed that she was a CIA employee (including her name), it was part of the story.
Releasing her name, in light of the fact that so many people in Washington D.C. (and even Mr. Wilson's own biography) knew her name and what she did might not have been the best journalistic decision, but it was hardly "do not publish" information. Even the CIA said that they would prefer that he didn't release the name, but didn't insist on it.
Novak, while maintaining his journalistic intregrity, would have likely excluded the name if the CIA explained the potential national security issue. He would have likely said, "Wilson, whose wife works with CIA..." The fact (indisputable fact) is that the CIA didn't do so...they merely preferred that he not mention it.
You are taking Novak at his word. But this is a bit inconsistent with the CIA requesting the investigation.