Unfortunately that is not isolated to JNB but alot of the African airports are like this, I have heard horror stories from REVENUE passengers in Lagos, Abuja etc., etc.
I have always wanted to visit South Africa but I would stay away from the nonstops to the US on DL or SAA, namely becasue I am sure this has got to be one of the toughest flights in the DL system to get on (because of heavy loads, high nonrev count, and possible weight penalty issues with the aircraft).
Other than the bad service on EK, was it easy to get on the flight from JNB to DXB on Emirates or did they put you through hoops to get on the flight.?

Regards,

Chepos