The New York Times Public Editor, Margaret Sullivan, agrees that Rick Perlstein was unfairly swift-boated  here, and that the NYT contributed to the problem. See her post today: “Was an Accusation of Plagiarism Really a Political Attack?” 
Sullivan discussed the matter with NYT deputy media editor Bill Brink, who, rather incredibly, said
We wrote about it because it was out there and thought we could take it head-on in the story.
It was out there.
What’s so wrong about that — and what Bill Brink should know already, in his bones, if he’s working in journalism — is that there is no out there.
To act as though there’s such a thing as out there, and to think that one can just report on whatever’s happening out there, is merely to enable the rumor-spreaders and gossip-mongers who are the enemy of truth-seeking journalists. This is easy to see by induction: if Rick Perlstein didn’t engage in plagiarism (which he didn’t), but the NYT prints an article saying that he’s been accused of it, does that mean it’s now “out there”? And now that it’s out there, that would justify an editor at, say, CNN doing a quick spot on it too? Fair game, because it’s out there now, right? Meanwhile, the false charge gains credibility with every ratchet-step in prestige of the outlet repeating it. So walk back the cat: whatever source the NYT got the charges from has to evaluated, like any other source, and not be amplified if not credible. But instead, the NYT just played a middle step in a rumor chain.
Repeating rumors is not journalism. If the story is about the fact that a rumor is circulating, then clearly state that — meta is okay, though it should be reserved for very rare cases (this wasn’t one of them) where the effect of the rumor is itself a story. And the responsible way to report on those cases is to actually evaluate the evidence for and against the rumor, while making it clear that the story is about why the rumor is circulating. If the rumor has no basis in fact, that absolutely must be made unambiguously clear in the story, preferably in the lede. Quick test: if your story isn’t promoting the circulation of something true and discouraging the circulation of something false, you’re doing it wrong.
The original NYT piece didn’t meet any of these tests. As Margaret Sullivan rightly says:
Yes, the claim was “out there” but so are smears of all kinds as well as claims that the earth is flat and that climate change is unfounded. This one comes from the author of a book on the same subject with an opposing political orientation. By taking it seriously, The Times conferred a legitimacy on the accusation it would not otherwise have had.
And while it is true that Mr. Perlstein and his publisher were given plenty of opportunity to respond, that doesn’t help much. It’s as if The Times is saying: Here’s an accusation; here’s a denial; and, heck, we don’t really know. We’re staying out of it. Readers frequently complain to me about this he said, she said false equivalency — and for good reason.
So I’m with the critics. The Times article amplified a damaging accusation of plagiarism without establishing its validity and doing so in a way that is transparent to the reader. The standard has to be higher.
If Bill Brink still doesn’t understand this, even after reading Sullivan’s piece, he’s in the wrong job