I have heard that although SA is an ICAO member state its CAA is not regarded particularly highly by the JAA. Having said that, commercial pilots receive excellent training out there and most of the problems with international recognition relate to the background administration rather than frontline piloting.
Any SA ATPL holder would need to do a time-consuming and costly conversion to fly in JAA countries, but I know of at least one guy whose company paid for it.
Good luck.