So as far as I can tell from the article, there's corporate- or size-based discrimination, but mostly not content-based discrimination. Which is to say, if BoingBoing said they thought the government was peachy-keen, they still wouldn't be journalists in the eyes of the DOJ, they're "mere" bloggers. But if the NYTimes published a policy critique embarassing to the government, they would still be journalists in the eyes of the DOJ, and still merit journalistic protection.
Content-based exemptions to protection from search arise when the content in question is secret government information whose disclosure is not authorized.
So, yes, this is troubling, it ratifies the special status of corporate media, who are famously spineless in protecting their access, and there's obvious potential for abuse in the "unauthorized disclosure" provision -- the government can make all journalism a crime by classifying mundane policy discussions. (Remember Dick Cheney's secret energy policy team?)
But it's not (yet) communist-style content controls.
It reminds me of the balance-striking problems with campaign-finance -- at what point does policy advocacy become partisan campaigning, or even lobbying? If you have campaign-finance regulations, where do they stop? Similarly, once you define journalism, when do you stop?