I'm not an airline employee but I am a SAA frequent flyer. I'm an American who has lived in South Africa for the last 12 years and I must say, on the whole, South African Airways is hands down better than any airline I ever flew in the US in terms of being on time, courtesy of the cabin crew and amenities offered. However, I do tell any of my friends who fly SAA though Joburg to collect their baggage and recheck it if their layover is more than a couple hours. Several years ago there was a serious problem at OR Tambo airport with bags being stolen and pilfered from but they've changed the handling company and things have improved dramatically. I would suggest you also seek recompense from the Airports Company of South Africa (
http://www.acsa.co.za/home.asp?pid=3634) who employ the baggage handlers.
Not to diminish your hardship, have you checked the SAA baggage liability and conditions on their web site? They specifically say that valuables are not to be included in checked baggage. There are also international conventions that limit their liability in this regard and I believe it's much closer to the $400 you received than the $2000 you claimed.