What they did was they interviewed people who know relevant stuff. And then they quoted what those people said about the relevant stuff. Where I come from, we call that reporting.
The fact that they quote stuff about her character in an article about her character is... not very surprising.

This was an article about her character?

You are seriously insisting that Ms. McCarthy is in the news only to profile her character???!?!

Maybe you didn't notice: she lost her job because she leaked Top Secret information that harmed our ability to share intelligence with our allies. I'd think the idea that she's "good", "independent", and "good, substantive person" might not quite be as important as her political connections and the fact that she gave at least $7000 to help end her boss' administration...which she then followed up with leaking classified information to undermine his policies.

Ya think that might be a teensy bit more relevent than someone's obviously incorrect opinion that "she's never deviated from the rules"?

Was that stuff NOT mentioned in the article at all? Or was it just "Here are all the good things about this person, apropos of nothing". Misquotation, the saviour of all stinky Broadway productions since forever.

Well, those allegations are unproven and based primarily on a polygraph test. The article wasn't investigative reporting about the accusations, it was an article about her character. And only one of those quotes is not in quotations within the article, so it's not that NYTimes likes MM, it's that the CIA does.

In a job such as the one she was in, she is subject to an annual counterintelligence polygraph. She signed a waiver that said that she accepts that her job was contingent on satisfactorily passing the poly. So, even if they can't or won't document specifics, they don't really have to. They prep you prior to the exam, telling you several times what the questions are that they are going to ask. If after all of this prep, you are still uncomfortable with your answer, then this is deemed unsat.

DISCLAIMER: I didn't read the article.