The defamation suit is claiming that his attempt to de-anonymize her false-positive-associated some reprehensible things said on another site with her, which she did not say. She isn't disputing that she said the things on the Disqus forum (or several other things on other sites).

She's either telling the truth or she's gambling that he overplayed his hand, doesn't have hard evidence to link her to those comments, and (in the context of a civil suit, which is what defamation is) lacks the resources to prove his case with preponderance of evidence. In which case, he'll be liable for damages and have to pay to "make her whole" (which could be quite a bit if she can convince the court she lost her job because of the things she's alleged to have said in that one set of comments she's suing over).

The only thing I can think of is that maybe she had some expected right to privacy that he violated on behalf of Neiman Labs?

Either that or maybe she can demonstrate how his actions caused her harm without her harming him, but his actions were only possible as an employee of Neiman labs.

I think what will most likely happen is he will be fired and she will get an undisclosed settlement.