They'd probably just be repatriated to either Germany or Mittelafrika. If anything, I can see South Africa playing nice with Germany, and pushing the boundaries of their ability to conduct foreign affairs without sanction from London to cozy up to Berlin.
I have to agree. Sudwestafrika / Namibia is primarily desert and was never that attractive for European settlement. I'm sure some of the few German colonists in the region are not pleased with now being a part of South Africa, but they are so few in number that I don't see any chance for a meaningful resistance.
From the perspective of South Africa, I can see them treating the Germans in Namibia that choose to stay with velvet gloves. South Africa has always been generally pro white immigration and German and Dutch are sister languages. The Boers have obvious incentives to treat German settlers with kindness.
South Africa also has a fierce independent streak and getting into the good graces of a major industrial power like Germany to act a counterpoint to overbearing British dominance is a no brainer.
Remember that Britain just lost a major war. Even if the terms they had to pay were very lenient, the damage to their pride and image should not be understated. The war has perfectly illustrated just how limited and utterly worthless are many of their "promises" - just ask France. I can see South Africa flexing their diplomatic muscles and daring Britain to say something to the contrary.
If something major happens (like a full scale revolution in the British Raj) then all bets are off.