Maybe I'm giving him too much credit, but I think the author's emphasizing that the term itself sounds like damning evidence to anyone who doesn't know better, since subversion means "a systematic attempt to overthrow or undermine a government or political system by persons working secretly from within." He's pointing out that agent used such terms without understanding them (or exploited the public's ignorance to make their case). That's why he put it in quotes.
Lewis goes on to explain, later in the article, that subversion repositories are commonly used and aren't evil. He could have explicitly spelled out that the term subversion relates to version control, but I think he explained it adequately enough given the intended audience.
Oh, I agree, but the point the article seemed to be making was that the agent thought it was fishy that the name of the repo was "subversion", rather than "github" or "bobs-useless-code-dump". It was a complete misunderstanding of what was important (storing code elsewhere), and an ascribing of malicious intent ("subversive") to it.
Lewis goes on to explain, later in the article, that subversion repositories are commonly used and aren't evil. He could have explicitly spelled out that the term subversion relates to version control, but I think he explained it adequately enough given the intended audience.