IMO one of the rules that all agents handling BA check-in should know is that if they cancel a flight then they sort it out, not tell the passenger to go and sort it out with the non-operating carrier which has absolutely no representation at JNB and only GSAs in the entire continent of Africa. To me the initial response of the agent was not due to lack of knowledge but absolute lack of interest in providing essential customer service to one of their passengers.
Of all the things that are posted as complaints/heads-up for FTers this seems to me to be one of the more reasonable ones.