I flew from DC on the SAA direct flight to JNB it does a stop in Dakar but we stayed on the plane for the hour - a good break to stretch. the rerun JNB to JFK was easy and the airport both sides easy to navigate/get bags.
One thing to watch out for are all of the aggressive "helpers" in JNB to push your luggage cart for a tip. They annoyed me and I had to yell at one guy to leave me alone as a solo traveler.