I don't fully understand Rwanda's screwy logic for aviation and sub-contracting.
I believe they had been contracting out the Kigali - Johannesburg flight at various points, at first it was operated with an MD-80 series aircraft and then a 737.
For someplace that is marketing themselves as progressive in East Africa, Rwanda also makes it exceedingly difficult to obtain overflight clearances.
Didn't SAA used to do some sort of JNB - KGL - EBB - JNB route a couple years ago?