I think your best option would be to send your passport back and someone collects on your behalf. Provided that it has been issued by then. I'm not sure if you can have 2 applications in the system for the same Visa. I'm sorry on this one I cant advise further because your visa has taken way too long to come out which is odd for an SA application and you have travel plans.
Ideally you don't leave SA till you have a visa in hand . But you had made plans already. So maybe Obiyepeh can advise.