Which type of response from the blog owner do you think would be more likely to convince you that he was not actually an anti-Semite: 1) deleting the comment, covering up its existence, and never speaking of it, or 2) Leaving the comment in place, and refuting it - carefully laying out why the commenter is wrong.

If someone really wants to get some cheap internet points for accusing the author of antisemitism, either option can be used. In both cases, the fact that the comment was written on the blog would be interpreted as an evidence for blog somehow evoking this kind of comment. Both deleting and refuting would be interpreted like "the author pretends to disagree, for obvious PR reasons, but he cannot fool us".

The advantage of deleting the comment is that a potential accuser has smaller chance to notice it (well, unless some readers make "why did this specific comment disappear?" their topic of the month), and they cannot support their attacks with hyperlinks and screenshots. Also, if someone puts specific keywords in Google, they will not get that blog among results.