The fear wasn't retribution against the former government. The fear was what the ANC and its leadership (or whatever might follow, because nobody knew what was going to happen) might do with full access to the nuclear/chemical/bio programs RSA engaged in.
Tribal dynamics are still a very real thing there, and it's not inconceivable that a leader might decide to slime those jerks across the way that have been rivals since well before colonists showed up.
The were very real concerns within the apartheid government about a racial civil war: not everyone in the government was convinced that ending apartheid was a great idea.
You also have to remember why the apartheid government developed the nuclear/bio/chemical programs in the first place, and who they considered to be their enemies - looking at the range of the respective payload delivery platforms (or lack thereof) should give you a hint.
> Tribal dynamics are still a very real thing there[...]
...and the apartheid intelligence apparatus fanned those flames of division to the bitter end, by supporting, and providing training for the IFP militia[1] to put the ANC on the back foot.
> [...] it's not inconceivable that a leader might decide to slime those jerks across the way that have been rivals since well before colonists showed up.
The apartheid government didn't consider black people to be citizens of South Africa, instead, they were regarded as citizens of balkanized Bantustans which were supposedly sovereign enclaves, divided by tribe, and forcibly moved (by the apartheid government). I have great difficulty believing the same apartheid government was motivated to denuclearize in order to avoid inter-tribal strife.
At the end of the program, the primary reason RSA developed nuclear weapons was to force the hand of Western powers into interceding if RSA was losing a conventional war (help us or we'll start nuking cities).
They had zero interest in detonating a nuclear weapon just to kill black people, especially not on their own territory. RSA intelligence services certainly investigated things like race-specific diseases, but that's not what the nuke program was for.
