They aren't pretending it's gone. There is a difference between a journalist passively receiving classified material which a source decides to provide them and a journalist actively soliciting a source to provide classified material. The government has a reasonable argument that a journalist actively soliciting for classified material may be in violation of the law and not protected under the first amendment. This has not been settled by case law and the judge which signed off on the search warrant agreed with the government that the journalist may be a co-conspirator.