Hi Faerie!
I generally only lurk around here, and very rarely feel the need to post anything. However your thread has struck a chord with me because I was in the same position as your son. I also hail from the same area as you guys, and know the schools and types of people there well. In short I sympathise

. In all likelihood a secretary took one look at your application and threw it in the bin. It’s their job and we understand, good for them, but we DO NOT have to except that

.
I applied to go to Wits a mere 4 years ago; the rules haven’t changed at all and entrance requirements are the same, meaning there’s a time limit on applications and blah blah blah. These “rules” did not stop me from barging in there in the middle of January to apply. I still got in that year; all it took was the will to do so. I urge your son not to give up, at least not until he has gotten thrown out by security.
The Faculty Dean has the power to enrol you anytime before the start of the courses even by only 1 day. Let your son go to him/her mano-a-mano. It is imperative that he go alone. Your presence there will only confirm to them that this is your choice not his, understandable, a mother wants only the best for her son.
Of course I’m assuming your son has the determination to do this, and pull through years of hard work. But in our country and in this climate can he afford not to? Please don’t be despondent, it’s still waaayyyy to early in the fight! You still have LOTS of time!