I don't know what exactly the SAAF requires, but I can tell you that much: since I left school no one ever cared to see my high school certificate ever. To grasp all of the concepts in aviation basic physics and basic maths is enough, too.
For your particular case I'd probably keep the science course, it can't hurt to have a broader knowledge in both, maths and science. But in the end, what it really comes down to, is good mental arithmetics, trigonometry and an understanding of basic equations that you might come across - this is nothing but practice. And of course basic physics.
Pilots just don't tell anyone that their study courses are not rocket science but could be accomplished by a 7th-grader
What's important is that you try to strive for the best you can possibly achieve with the greatest effort you can put in - these core-values are more important in this industry than any high school diploma.