I tought that there was foul play too, but in fact it is pretty straightforward.
Bizarrely, it seems like some people try make this looks like a race issue, when the majority of the athletes who had the standard and who were not selected are actually non-White (even amongst those names linked in the OP which somehow forgets quite a few name).
here is a link of all the SA athletes who hit a qualifying time and were not selected :
http://roadto.de/mycountry.php?nat=RSA
Keep in my mind that many of these "screwed" athletes barely got the standard in a rather weak event in their country. Does a female sprinter who barely run sub 23 over 200m deserves more her place that a 20"2 male sprinter simply because her event is incredibly weak ?
In the male 200m, the 6th ranked SA sprinter ran 20"27, a time that would have qualified him in pretty much every country in the World (including sprint powerhouse Jamaica), but he won't make the team because this event is stacked in his country.
I mean, do you know that the Bronze medallist in this event at the last Wch in 2015 (Jobodwana 19"87), behind Bolt & Gatlin is not even ranked in top five anymore. Yet he would still be much more threatening that many of those non selected athletes.
Pretty much all the athlete who have a chance of a medal or reaching a final were included in the original team, because they hit the (tougher) qualifying standard that was set by their federation several month ago (including a non-Black one one who shouldn't, because his standard was achieved during a competition where he tested positive afterwards).
BTW, several country have their own standards, if you've been following this sport for quite a long time this is nothing new.