the fundamental problem here is that the blacks are less educated (and less a lot of other things related to education) than whites.
That is a large part of the fundamental problem, yes. A lot of blacks were also:
And the education problem is made worse by the fact that there were not enough properly qualified teachers in the country to deliver that education to everyone.
And you are right, these problems are not going to get resolved quickly. (It's twenty years later now, and a lot of the problems still haven't been resolved). It's probably going to take two, maybe three generations minimum to get the country back on an even keel again.
But, in short, Apartheid was an incredibly unbalanced system. The inequalities caused and perpetuated during the Apartheid years were massive, dwarfing any possible genetic differences in intelligence. And, in the face of those inequalities, it seems to me that a temporary program of affirmative action (defined as, if there are muliple qualified applicants for a position, bias the selection process in the direction of the black applicants if present) is a reasonable measure to try to counteract those inequalities without sabotaging the country's economy.
Compare apartheid with feudalism. And notice that a lot of countries transitioned away from the latter didn't require AA in favor of commoners.
Suppose I told you that I knew for a fact that the following statements were true:
You’d think I was crazy, right?
Now suppose it were the year 1901, and you had to choose between believing those statements I have just offered, and believing statements like the following:
Based on a comment of Robin Hanson’s: “I wonder if one could describe in enough detail a fictional story of an alternative reality, a reality that our ancestors could not distinguish from the truth, in order to make it very clear how surprising the truth turned out to be.”1
1Source: http://lesswrong.com/lw/j0/making_history_available/ewg.