They are moving the A346 to JNB/PER which is an expanding route with far less competition. That is what they have stated
Don't forget that every European airline that goes to JNB does (or wants to) go to CPT. Then there are the Middle Eastern connections.
Further, my guess, is that the UK holiday market for ZA may have run it's course. The route has been heavily operated for 15 years and the other new folks piling in, I can see why they might want to give it up.
They are also making other changes in their global and African routes.