Why haven't there been more Espionage Act prosecutions? One reason is that the government often fears a trial will reveal secret information. Another is that there is a widespread consensus that there is rampant overclassification -- the government sometimes classifies newspaper articles, but it isn't going to prosecute anyone for leaking them.
But the NSA surveillance and the secret prisons were things the government definitely wanted kept secret, and it has argued plausibly that their publication has damaged the interests of the United States. Bill Keller and Leonard Downie, the highly respected top editors of the Times and the Post, have said that they decided publication wouldn't hurt national security. But the law, perhaps unwisely, doesn't give them the final decision on that.
There have been only a few leak prosecutions under the Espionage Act. A retired CIA analyst was convicted for leaking documents to Jane's Fighting Ships in 1984. Defense Department employee Lawrence Franklin was sentenced in January to 12-and-a-half years in prison for disclosing classified information to two employees of the American Israel Public Affairs Committee. A prosecution is underway of the two recipients of the leak, who stand in the same legal shoes as the Times and Post reporters.
In effect, there has been an informal truce between prosecutors and the press -- Justice Department guidelines discourage asking reporters about sources. But in the Novak leak case, the press's demands for an investigation led to just such questioning.
So now the government can make a case for prosecution by quoting the Times' editorials on the Novak leak case. It's certainly plausible that there was much less damage to national security in that case than in the NSA and secret prison stories. There's an argument here for government forbearance: Prosecutions will dry up a lot of sources. But there's also an argument for forbearance by the papers. An argument about blowback.