This article is absolutely right that mainstream news coverage is taking the government's side, rather than discussing the issue itself. The NSA 'scandal' is a good example. By calling it a scandal, that's already taking the side of the US government. The public should have the right to know this is happening, but has any coverage expressed that what Snowden did was a good thing? I'm not sure, but I'd guess probably not, or not as much as they should be. And if they did, that would be a good start at trying to be 'objective.'
However, older reporters may not have the same views as younger ones. And "adversarial journalists" are not something that more traditional journalists may understand. When Andrew Ross Sorkin said he thought blogger, Glen Greenwald should be arrested on live TV, wasn't that advocating as well?
I'll say that the line between advocacy and journalism is a thin one, but as long as you're reporting the facts, I think it's acceptable.