If the movie had tried to make some overt statement about Apartheid we'd have tons of people screaming it was going for a cheap sensationalism angle by having such a /serious/ issue in a mere sci-fi flick. So in hindsight I think Blomkamp made the right call.
Besides, South Africa today isn't the one of 28 years ago, and while its history is very important, this is an entertainment film. Not a film that exists just to promote a political message. As it stands, this movie still has a far more authentic look at the general aura of modern day South Africa than most of what you see (which should say something terrible about most of what you see).
Not to pull a rank card (really) but I can remark for trivia that my significant other comes from South Africa originally and gives the film a big thumbs up for how it uses the country as a backdrop.