And that's precisely what the movie shows.
Yes, killing a slave would have been stupid. Systematically raping them, on the other hand, made good business sense--as long as you have no qualms about treating your own offspring as slaves, which antebellum southerners evidently didn't. Savagely beating them for the slightest infractions made sense too, since it was (reasonably enough) deemed necessary to constantly terrorize them in order to keep them subjugated.
And the entire system was predicated on the assumption that slaves were not fully human--were in fact animals, and to be treated as such--and that's the major point the movie is making.
I've heard many people minimize the evils of slavery: "oh, they'd have been slaves in Africa anyway, oh their descendendents are better off than modern-day Africans, oh they really weren't whipped all that much..." I'm sure you've heard similar. Well no-one will say such things after watching GUT. I reall think it's a work of genius.