I realize, in general - apartheid, I get it. But was there anything more subtle that someone closer to the culture and politics in South Africa picked up that general audiences around the world would not?
I think the film may be making more of a general statement regarding the feelings of South Africa regarding issues with illegal immigration, first from Rhodesia and then from Zimbabwe, Mozambique, and Nigeria. As I understand it they have major issues with South Africans lashing out at the migrants in the form of riots. As a response to this a number of camps were established to "house" the migrants.
This story from the BBC website gives more specific details. The general description of the camps sounds disturbingly similar to the conditions of District 9. These events (riots and camps) occurred in 2008.
I'm not convinced the film is even really concerned with apartheid. It's concerned primarily with an external population coming in and creating a nuisance (as opposed to apartheid where an external population came in and totally rebuilt society).
I think the key point of the film is how do you deal with major humanitarian\xenotarian issues. If you a have a population that moves in and brings tens\hundreds of thousands of beings with no means to survive how do you assimilate that. What if the migrant population DOESN'T want to assimilate but retain their own cultural values in the face of an established society? Do you allow them to starve on the street? Do you evict them to a fate of certain death or torture. If there is no land willing to accept them do you march them into the sea? If your own population rejects their presence do you allow said "native" population to murder the migrants in the street?
I think the film (or at least the first half of the film) is really just trying to shock people into seeing the major issues associated with migrant populations\refuges.
It's less apartheid and more contemporary South Africa - the aliens represent Zimbabwean immigrants.
"I was asking black South Africans about black Nigerians and Zimbabweans. That's actually where the idea came from was there are aliens living in South Africa, I asked "What do you feel about Zimbabwean Africans living here?" And those answers — they weren't actors, those are real answers..."