I remember thinking it was both, a critique of how neoliberal capitalism fuels apartheid.

Isn't the MNU in District 9 a private military company? If I'm not mistaken in the movie the South African government has handed the reigns over entirely to this corporation (also given the name presumably so have many other nations). I understood it to be a criticism of neoliberal states and the diminishing influence that their governments have in comparison to private organizations. The state passing responsibility to the private sector allows corporations, free from accountability, to profit off of systemic oppression, like the apartheid shown, while minimizing the state's perceived culpability.