Hi Shonna,
A child can learn a second language from 3 years old with no problems. By then the first language is set as the strongest language (granted that it is the language both parents use). I would suggest you continue speaking to him in your mother tongue. He will pick up on the afrikaans on his own time.
My little girl joined an english school when she was 3 years old and we are afrikaans.
It took her about 7 months to start speaking english. We speak to her in afrikaans at home.
Maybe at first he might be a bit "disorientated" by not understanding the language but I doubt that he will suffer emotional development issues. My LG is much happier in this school (english) school that she ever was in her previous afrikaans school.
This is just my experience from what I have researched.