I took handguns on both of my trips to RSA (T/C Encore, Ruger Super Redhawk). There was no drama at all. Our flights were different each time as we used airline miles for the first trip where we went DFW-Madrid-Joburg on AA and Iberia. The second time was Delta DFW-ATL-JNB. The TSA people were great both times.
I wholeheartedly agree with the previous posts regarding the use of a service that will help you get the permits cleared ahead of time, regardless of the type of gun, as it makes it real easy to get through the South Africa Police office. I've seen it mentioned that the handguns have to have scopes on them but my Ruger never did though I did have one in the gun case, just in case.
Depending on who checks your guns coming back w/ SAP, you may get subtle hints that they deserve a tip, such as "Do you have anything else for us?" I just played like I didn't hear them. Besides, it's supposed to be illegal for them to ask for tips so you probably won't hear them put it in those words.
The only slow part was coming back into country getting through customs in ATL. They weren't the speediest folks in the world so don't make your connections too tight.