There's a tiny little bit of a difference between 'the villains kill various members of team good' and whatever this stuff is:
“Hey, Draco, you know what I bet is even better for becoming friends than exchanging secrets? Committing murder.” “I have a tutor who says that,” Draco allowed. He reached inside his robes and scratched himself with an easy, natural motion. “Who’ve you got in mind?” Harry slammed The Quibbler down hard on the picnic table. “The guy who came up with this headline.” Draco groaned. “Not a guy. A girl. A ten-year-old girl, can you believe it? She went nuts after her mother died and her father, who owns this newspaper, is convinced that she’s a seer, so when he doesn’t know he asks Luna Lovegood and believes anything she says.” … Draco snarled. “She has some sort of perverse obsession about the Malfoys, too, and her father is politically opposed to us so he prints every word. As soon as I’m old enough I’m going to rape her.”
Also it's been many many years since I've read the books, but I don't remember a whole lot of killing on the parts of the heroes; a quick check of the Harry Potter wiki confirms that Neville killed Scabior, Molly Weasley killed Bellatrix, and various monsters bit it; I'm also going to choose not to count the obvious other example on grounds of intent.
That was a very clumsily executed attempt at shocking the reader by showing how messed up the Malfoy family is, by indirectly informing the reader that Draco believes he is above the law and has no compassion. I don't think there's much more you can read into it
What do you mean by 'rapey' then? There's no way the book was on Draco's side when he made that comment. And I'm not sure what you mean by 'the whole Bellatrix stuff', but wasn't she a victim of the evil antagonist? If you think those bits were awkward, inappropriate, badly written, ineptly conceived, or whatever, I'm sure you'll find plenty of agreement. But calling the book 'rapey' seems to imply that it displays some kind of pro-rape message or attitude. That's a really harsh claim to make without strong evidence.
edit: maybe you just mean that it contains gratuitous references to rape? I guess that's a fair opinion to hold, but I think it's clear that the Draco thing wasn't included for the fun of it, but was intended to show how messed up his upbringing/society was in a way that would genuinely shock the reader. And I can't remember exactly what happened to Bellatrix, but I also don't remember getting the sense that the book was revelling in the grisly details or anything like that.