I think Eliezer has got the meaning more or less right. When Daniel asked "what it meant," I assumed he was merely referring to the idiom, not the entire quote.

So is it saying that epistemology should not allow for equal punishments for unequal crimes? That seems less like epistemology and more like ethics.

As an example of the kind of thing I think the quote is warning against, the theist philosopher Plantinga holds (I'm paraphrasing somewhat uncharitably) that believing in the existence of other minds (i.e., believing that other people are conscious) requires a certain leap of faith which is not justified by empirical evidence. Therefore, theists are not any worse off than everybody else when they make the leap to a god.