Maybe I'm being a bit thick here, but surely it's up to VS as the carrier and ticket issuer if they decide to honour the LHR-JNB even if you agree in advance to no-show for the BSL-LHR. So why can't you just call VS, explain that BA have cancelled the flight and this renders your trip to BSL pointless as you cannot reschedule to the later BSL-LHR-JNB, and can they override the no-show that will presumably be triggered by BA if you just rock up at LHR. At most you will have £75-£150 in long haul APD to pay but that has to be less than the cost of a positioning flight and a hotel, not to mention your time.

For the record I've done this on BA to BA metal before (LGW-JER positioning flight delayed, meant the JER-LGW was so delayed I'd have missed the onward to JFK, BA would have been hit for max EC261 comp so were quite happy to override the no-show) and there are plenty of examples on this board where they have too. And that's where BA are very strict as they don't want to encourage it.

Virgin on the other hand probably don't really care if you don't show for the BA flight, as long as you're not asking them to reimburse you for that leg.

But you must agree it in writing in advance!