There does not seem to be a convincing reason in principle not to prosecute the Times for espionage and treason.
This reductio ad absurdum is worth exploring to illustrate the absurdity of the situation we are now in. The United States government for all intents and purposes is legally unable to protect classified information, safeguard national security, and prosecute leaks. The one tool it has -- the Espionage Act -- is a nearly century-old statute that is so draconian, politically radioactive, and difficult to implement that it is essentially defunct.
As I said before: The primary consequence of Wikileaks will be the tools, process, and laws that will be used in the future to suppress other leaks.