No Border War might prolong Apartheid, but it isn't going to last forever. It is, after all, an inherently contradictory system: disenfranchising huge amounts of the populace is still having huge aftereffects on the South African economy today. And, honestly, once the noose started to tighten around the Apartheid regime with regards to major, across-the-board sanctions in the 80's, the Apartheid system's borrowed time got even shorter.
In short, I see things like the economic strains created by the Border War as a symptom rather than a cause of the disease: Apartheid as a whole was untenable. And, really, the longer it goes on, the more likely it will be that people like Mandela get marginalized and the whole thing ends violently.