Many transcripts between Botha and parliament reveal the actual truth. We hide it right now as an act of humanity and as such it was, because it still took a great amount of trust to pursue.

The government at the time was under immense pressure as I'm sure you are aware of, with economic and sport sanctions being the norm our country was effectively isolated. The government at the time almost turned a blind eye to the glaring issues. Unfortunate as it was. But thankfully many people saw the holes, the cracks, the gaping issues flooding into South Africa as a whole. Many officials could see the end of Apartheid was close by 1988 around. The talks were to dismantle the WMDs and ensure that all research should be cleared so that the new government, most likely communist (this was thought to be true) would not be able to use this. There were many other sources of pressure, America had its hand here, Australia too, to push for the presence of WMDs to be removed. 1989 happening was almost like the last straw. Communism as a threat, not as a whole, was disappearing and suddenly the urge to keep WMDs from the East ceased slightly and turned to keeping it from the new government. What is difficult to understand is the mentality of the government and average person. Nobody knew what kind of government would take over after Botha, after the NP etc. Tensions were pretty high but mostly it came down to the Afrikaners worried that a new government would use the WMDs for the incorrect reasons. I suppose I can see where they are coming from.

You can read up more about it here, it's actually extremely helpful. http://uir.unisa.ac.za/handle/10500/13313 and you can read here to learn about the 'sport' sanctions and how Apartheid affected South Africa's teams.