Various airlines have tried alterations on this, to improve utilisation; Swiss does (or certainly did, at one stage) have a morning departure from ZRH, which allows a short turnaround at JNB. Virgin also has some daylight returns from CPT.
I guess one of the issues is that they want to maximise connections (where can you connect if you get into LHR at about 9pm at night?) and there may well be a pax preference issue.
It must be a pain for airlines to have an asset on the ground all day, but I guess the point is that they do try various other scheduling options, but most still choose the long day stop in JNB.