Look at Air Berlin too. They fly direct from Munich to Windhoek, so you'd still have to transit through Germany. I haven't flown them before but I've started to look at them for future travel as they have some very reasonable rates.
I keep hoping that one of the U.S.-based airlines will offer a direct flight from the States to Windhoek (think Delta: ATL - WDH). Should be doable with 777-ER's as it's closer than RSA.
