The codeshares never can go away as they are specified in the route authority for both QF and SA. Apparently both governments were concerned about having adequate service, and SA back then didn't have the planes to fly JNB-SYD non-stop (did fly JNB-PER-SYD but that wasn't profitable), thus this arrangement came to be (codeshares, with QF staying out of PER-JNB service) and etched in stone by the governments. It is a case where airline and national interests had priority over alliance interests.