You are far off-base when you say "apparently just fine". But making the thread still more uncivil is obviously the wrong thing to do. Better things include: (1) make an accurate, respectful reply—though in this case it would have probably blown things further off-topic; (2) flag the comment; (3) email us at hn@ycombinator.com.
If you can find the will to do so, the very best thing is to be charitable. In this case that might mean remembering that the commenter has likely only heard one heavily politicized side of the story, and has been conditioned by such one-sided information to reflexively associate one thing with another. Then you might respond in a way that confounds their expectation in a positive, surprising manner, instead of getting angry and defensive, which can only reinforce it.
Admittedly that's hard to do and never something one must do. But it is likely the most effective thing to do. When one person responds from a conditioned reflex but another has the presence not to do so, that's how things get unstuck.
The demographics of HN are so unevenly distributed that it's impossible for the discourse here to be objective about many topics, but we can and do at least control for basic respect, and if you watch closely you'll notice that we care about that, and act on it, a lot.