In terms of non-stop and one-stop, SAA flies to both JFK and IAD from JNB. JFK is non-stop in both directions, while IAD stops in either ACC or DKR (depending on the day of the week) in both directions.
Keep in mind that any transits through Europe are likely to result in very long layovers on the outbound leg in Europe (except KLM through AMS).
In terms of their onboard product, I find SAA's business class comparable, and sometimes even better than some European airlines, but not up to Middle Easter or Asian standards.
Don't forget Delta, they have a non-stop ATL to JNB.