I think the question is whether BA is responsible for getting the OP to JNB at its leisure, on on time. I'd vote for the latter and think that the OP has a valid basis for claiming a refund, although that's going to be a long and painful process.

I don't think that most insurance policies will cover this as they require a min 4h layover if on separate tickets (and in any case, I don't think that a passenger should go straight to the insurance company in such circumstances if it's primarily the airline's fault - it seems this was not weather related etc.).