The nuclear weapons program wasn't just for defense against communists, it was also to preserve apartheid. Although it started work ending the weapons program in the late 1980s, the apartheid government could try to reactivate it and threaten the use of nuclear weapons to bring about a desirable outcome through foreign intervention.
I don't think that would work, nor in the event even be attempted.
But more practically the nuclear weapons would keep outside powers from intervening.
Yeah, not with the leadership that existed within the South African government at the time, you'd have to get people who were more radical than De Klerk in to make a nuclear option a reality.
Vortex by Larry Bond is a pretty good depiction of a possible South African civil war in the early 1990s.
But I'm not sure that the assassination of Nelson Mandela will lead to a civil war, you might need to get some other things to go wrong.
A South African civil war will also be messy, it won't just be the white government versus black rebels. You would have government forces, ANC forces, IFP forces (Zulu nationalists), and probably right-wing whites fighting against the government and the ANC
et al.
EDIT: A plausible start for a civil war could be that the coup considered by Constand Viljoen in (I think) 1993 goes ahead. This will likely split the SADF, and may well see some elements in the homelands (especially Ciskei and Bophuthatswana) side with Viljoen (the leaders of these homelands didn't want to be reintegrated into South Africa). If negotiations end this will also see the ANC return to armed struggle.