I think rape is used to show "evil" mainly because it is one of the worse crimes we can commit against anyone. There really isn't much more worse, unless you involve children and I'm thankful writers as a whole avoid that specific topic. It is related to us, as readers, becoming jaded to crimes. It seems like most sci-fi worlds, besides our own, is populated with thousands of creatures that eat everyone, aggressiveness that we don't have in our own world. And crimes are the same way. Everyone seems to be getting mugged, attacked, drawn into nearly constant battles. Things are stolen and people are lost, mainly because stories are about the interesting events in a character's life, not the endless hours of sitting around playing cards. Rape is basically near the pinnacle of these crimes.

Personally, I'm not fond of writing about it. Actually, I don't write about it. I do think you can create a compelling story without it. It is a good way of setting the mood, or letting the reader fill in a lot more (internal struggle as you mention), but if it is overused by too many authors, I think it does become muted.

I was watching Serenity on Monday (bad movie night, though its a good movie) and I noticed the same thing. They kept hammering the point that Reavers rape women, and that was the major reason they were frightened. I think it was a plot device, but I found it, I don't have a good word, "bolted on" in a sense. It didn't add much to the story, it was just there to say "these are really bad people" like the rest of what the Reavers did was any worse.