If possible, I would try and avoid Air Namibia and SAA. While I have not flown Air Namibia since 2009 (relatively good experience), I have grown suspect of their inconsistencies and cancellations. Add to that, the fee for carrying firearms and I pretty much crossed AN off my list.
The KLM flight sounded like a good alternative but the Dutch, like the Germans, also require a transit permit when traveling with firearms. What really scared me away from KLM was that stop in Angola. It sounds like you do not get off the aircraft but I think I will pass on this route.
Look at Condor Air. They also fly direct to Windhoek from Frankfurt although not as frequently as Air Namibia. I used them last fall and was quite impressed - timely service, attentive on-board staff, and nice clean aircraft (they use Boeing 767's for this flight). I did not travel with a rifle but their firearms/ammunition policies are standard for the industry. They also have a baggage (inter-lining) agreement in place with Lufthansa. I am considering another hunt in Namibia this year and would use Condor again without hesitation.
