I know you are planning on going, so it's done. I know many families who visit with kids. It's great that you are going to visit familiy. They will know what to do, so I would just follow them. For intance, you can't go for walks, visit the park, all shopping is in secured malls. You can't stop on the side if the road for a bathroom break for the 3 year old. When you stop at say a service station, you get your fuel quickly. No walking around, taking the kids to the toilet, buying a snack. That is high risk behaviour.
Personally, I have 2 young children. I was born and grew up in JHB. I am dying for my family to meet my kids but I will not travel back to SA. My heart breaks over it, but it's just not safe and not a risk I'm willing to take. My kids will not understand how they can't go ride their bike, go to a park etc, have their window down in the car. Sorry for being such a downer just before your holiday, but it is a serious decision, especially that you're visiting JHB. Some South Africans think it's not too bad, they bury their head in the ground for survival, sometimes oblivious what is going on around them.