Cult quite explicitly means the latter, and is what the article is explicitly accusing the core of this community being (that is, not everyone reading LessWrong, but specifically the actual people living in the communes).

No one calls the Catholic Church "a cult", nor do they call, say, Zoroastrianism a cult (to pick a relatively small religion with weird practices).

I will note, if, like me, you're not a native English speaker, that there are two words, "cult" and "sect" that commonly exist in many European languages but often mean opposite things. That is, in English a "sect" is any "flavor" of a religion - catholicism and protestantism are sects of christianity; while "cult" describes closed off communities (usually of a religious nature) that are deemed harmful to their members. In my own native language, the two meanings are reversed - we use "cult" for "legitimate" religions, and "sectă" for closed off harmful religious communities.