Some thoughts..
South Africa is NOTHING like Australia. Don't expect it. Don't let your guard down.. even if it looks safe, civilised and friendly - it probably isn't. having said that.. millions of people live there, go about their day to day business, and survive, just like we do over here.
It's difficult to share a lifetime's thoughts, knowledge, prejudices and experiences in text.. but I'll try.. also please keep in mind, although I'm not trying to be racist, 90% of the threat is from non-white people..
Remember, your typical black South African is dirt poor.. poorer than you can imagine. Going to jail is an upgrade in lifestyle for him.. it means he'll sleep warm, and have 2 meals a day. In other words.. they literally have NOTHING to loose. Also, the police and justice system is fundamentally corrupt and overworked.. 90% of crimes will never be solved, of those where someone is apprehended, dockets will go missing, witnesses will stop caring, and the system will loose them somewhere.. it is only a fraction of a fraction that actually see the inside of a courtroom, or the inside of a jail.. again.. it boils down to.. they have nothing to be scared of, nothing to fear... if they want what you have, they'll take it. Almost always with more violence than you can imagine. Add to this a well developed hatred and mistrust of anyone white.. and you have a whole heap of fun.
Just to confuse the issue.. you have 1000's of law abiding black citizens that would love to just go about their business. They're friendly and caring just like anyone else in any other country.
So.. Sandton is in general probably the safest place to stay. The Holiday Inn is good, but there are a number of other hotels just as nice. A couple are right next to the Sandton City shopping complex - allowing you to go shop without going out into the streets.. maybe something worth thinking about. Having said that.. no point staying in Sandton if your work is 30kms away.. feel free to PM your address and I'll give you my opinion..
Don't go out at night.. not unless you're accompanied by locals.. personally.. I'd still stay home..
Don't take anything with you that you want to keep. Be prepared to loose everything.. watches, rings, jewellery, phones, cameras, wallets, credit cards, laptops, tablets etc..
Do get hold of an American Express card. For the simple reason, if your wallet gets stolen, Amex is probably the best in getting a new card to you ASAP. Often times within 24 hours. If you get a charge card.. so much better.. then you don't have to stress immediately about the cost of replacing what needs replacing.
Do let the locals organise your transport - if you have to rent a car.. go for something invisible.. don't drive a Merc or a BMW.. you'll stand out as a target !
Cape Town.. although CT is heaps better than Jo'burg.. it's still South Africa.. the difference is that the real poor areas in Cape Town are further away from the shopping / tourist areas than Jo'burg.. so the problem is not as visible.
Windhoek - what a lovely little city. I love the place.. all of Namibia is great. Do put the effort in to drive to Luderitz / Swakopmund. Go see the Etosha pans, and the desert elephants..
Finally.. go look on youtube or liveleak.com.. search for crime South Africa. .and watch some of the clips. Louis Theroux made a great documentary..
Watch that.. just to get some idea of what to expect..
If you're in Perth and want to pop over for a Braai ( South African BBQ ), and a chat, feel free..
Please stay safe.. it's a great country.. pity about the people.