Don't rely on the type of aircraft with the type of seats you want being available (and to be honest, I'm not entirely convinced that the upstairs economy seats with extra legroom exist on SAA).

Do you have any airline/alliance preferences? Is cost the deciding factor? If you're not too bothered about collecting miles and don't mind paying extra then a good travel agent might be able to get you a reasonable deal using Air Namibia who fly direct to Windhoek from either LGW (came as a surprise but a colleague has just done this) or FRA. You would probably end up using LH to get from ATL to FRA in the latter option.

BTW, I hope you enjoy long haul travel; with all the waiting around in airports, Windhoek is quite a trek, even from the UK. It's worth it though!