The DoJ investigations are premised on a request, and the requests come from outside. The Plame investigation started with a request from CIA, where the CIA request was prompted by Novak's article.
Reports are that the NSA investigation was "instigated" by a request from the NSA. We don't know when that request was transmitted to the DoJ. Pukin Dog asserts that the investigation predates publication, based on inside information.
Would there be an arrest and prosecution if the story had not been published? I think that's a good question, because without publication, an arrest and prosecution would serve to publicize the existence of the program. That doesn't mean the investigation would wait, only that the results of the investigation would be closely held until if and when needed.