…[but] consider cases where deontological considerations overrule utilitarian principles. For example, one might judge that it is bad to kill an innocent person even if his vital organs could be used to save five others who desperately need transplants. Here, arguably, we feel cumulatively more empathy for the five people in need than for the one healthy person, but our moral judgment does not track that empathetic response.

Not sure about this one, not least because I don't believe in deontology in the first place.

Second, consider the moral judgments one might issue from behind a Rawlsian veil of ignorance; you might decide it’s good to distribute resources to the needy because you might be needy. Here there is no empathy for the needy, but rather concern for the self.

Is a moral judgement that is made for the sole reason of self-interest a moral judgement?

Third, while on the topic of the self, consider cases in which you yourself are the victim of a moral transgression. You judge that you’ve been wronged, but you don’t thereby empathize with yourself, whatever that would mean.

Presumably you don't need to empathize with yourself, since you already have direct access to your own feelings.

Fourth, consider cases in which there is no salient victim. One can judge that it would be wrong to evade taxes or steal from a department store, for instance, without dwelling first on the suffering of those who would be harmed.

Actually a worthwhile point. Although empathy might make us care about victims in the first place, once that's established you just need to know that the action will result in victims to formulate a rule against it. This is because morality is about the victims, not about one's feelings about them.

Fifth, there are victimless transgressions, such as necrophilia, consensual sibling incest, destruction of (unpopulated) places in the environment, or desecration of a grave of someone who has no surviving relative. Empathy makes no sense in these cases.

Not terribly great examples, since I see no reason to care about most of these, but it is true that we're allowed to care about beautiful or interesting natural biomes for their own sake without "empathizing" with them, as we established in the previous "Not for the sake of X alone" discussions. (Although in most cases, destroying the place would have the effect of depriving possible future visitors of it, thereby creating victims.)