I had absolutely no problems with my JNB TA. They emailed me a proforma authorising the charges that I had to fax back to them. I also had to fax or email a copy of the picuture page of my passport.
Try
www.renniestravel.co.za
They are one of the biggest TA's in SA and are the Thomas Cook franchisee.
Edited to add that I have been to JNB may times and while I would not class it as "safe", if you take sensible precautions and do not walk around downtown at night then you will be fine. Staying in Sandton is your best bet.
[This message has been edited by Gaza (edited 08-08-2002).]