One trick that I noticed that adds considerable amount of 'spin' while allowing the article to remain factually correct is to present positive things about the group as subjective - coming from the group itself (which paints them as self-serving and lacking self-awareness), vague 'some' or (even better) some negatively characterized person (which taints it as unreliable), but to describe negative stuff as if it is objective and factual. Some examples:

"...the online persona he has publicly cultivated over the years—that of a gentle headmaster preparing to chaperone a rambunctious group of boys on a museum outing—but, in this case, it seemed to lend plausible deniability to what he surely knew would be taken as incitement." - ok, so his gentle manner is a "persona", but he "surely" incites his readers to harass journalists.

"Slate Star Codex is often held up as an example of what the well-behaved Internet can look like—a secret orchard of fruitful inquiry." - note the passive voice.

"Much of the support Alexander received was motivated simply by a love for his writing." - implies that the support was not founded on actual judgment of the situation.

"On the blog, Alexander strives to set an example as a sensitive, respectful, and humane interlocutor..." - note the word 'strives'. To be fair, the rest of the sentence is genuine praise for his skill as a writer.

"...the rationalists’ general willingness to pursue orderly exchanges on objectionable topics, often with monstrous people, remains not only a point of pride but a constitutive part of the subculture’s self-understanding." - note how willingness to pursue orderly exchanges (with people that are presented as objectively monstrous) is a subjective point of pride.

Compare:

"the business model of the Times has little to do with chasing “clicks,” per se, and, even if it did, no self-respecting journalist would conclude that the pursuit of clicks was best served by the de-anonymization of a "random blogger." - presented as a factual statement.

"...a near-pathological commitment to the reinvention of the wheel, using the language of game theory to explain, with mathematical rigor, some fact of social life that anyone trained in the humanities would likely accept as a given." - why is this commitment pathological? Why is it as worthless as presented?

"These conversations, about race and genetic or biological differences between the sexes, have rightfully drawn criticism from outsiders." - why was this criticism rightful?

"The rationalists regularly fail to reckon with power as it is practiced, or history as it has been experienced, and they indulge themselves in such contests with the freedom of those who have largely escaped discrimination." - fairly standard accusations of privilege presented as facts.

"there is some evidence to support the idea that he, like anyone, is wont to sacrifice rigor in moments of passion." - presented as a statement supported by evidence.

Similarly, concerns and worries of the group are presented as subjective, over-reacting and reaching into conspiracy theory territory. By contrast, worries that the group itself is problematic are presented as legitimate.

And of course 'rationalists' are consistently presented as low-status dorks, but I guess it is the usual New Yorker snobbery and not something nefarious.