Some further thoughts...
I think it actually is easier for many readers to justify/forgive a murderous character than a rapist. See, there are times where killing is justified: Self-defense, defense of others, during war, if the victim is truly evil and dangerous... Even if the murders committed by a specific character don't fall into those categories, the fact that some killing is justified may mitigate an element of the horror.
But rape? Rape is never justified. Never. Under no circumstances. Period.
It's also, by definition, a much more personal crime. Murder can be committed impersonally, at a distance, or swiftly. Rape cannot.
Finally, there's the simple fact that I can accept evil actions from evil characters more than I can from supposedly good, or even morally ambiguous characters. I've read and enjoyed novels that were basically about the villains, but that's because the author was clear about the fact that they were villains. I cannot accept a "hero," no matter how reluctant a hero he may be, committing rape. I don't want to read about a character like that, no matter how realistic he might be.
Don't know how much any of this enters into people's feelings about Covenant. I'm not even saying it impacts my reactions; I honestly don't know. It was just a thought that occurred that I figured I'd share.