gofer is certainly correct about South Africa and Namibia. Only point will be to watch out for the peak tourist season when FFM seats are in short supply. I am biased as I grew up in South Africa.
Getting from CPT to WDH (Windhoek, Namibia) is available on a number of carriers. SAA is a junior partner of Star A. and I have earnt mileage with them, although not tried claiming. Their website should inform.
If you do the Cape Province first, car hire from CPT up the first stage of the garden route and back is fabbo. Ask if you want more details. Then CPT to WDH, then to JNB for onward travel.
Incidentally, if you take up the LH to CPT idea, they do have some routings MUC (Munich) to CPT, two or three a week only but the advantage is that MUC is much smaller and quieter and up to date than FRA. I am biased as I worked in MUC for 18 months and know the airport well but it is a good one. After I had generated loads of miles on the LHR~MUC, I used them LHR~MUC~JNB in 'C' and was pleased. On the MUC to South Africa routes, they tend to use 340s but will run 74s if load demands.