Just a few thoughts about logistics:
- As departure date is a Sunday, traffic should not be a problem.
- There is indeed a left luggage facility at JNB.
- The Gautrain gets you into Sandton in less than half an hour.
- If your hotel is near the station (that includes the Radisson, Holiday Inn, IC, Michaelangelo etc.) it should be well less than an hour from JNB to your hotel room.
- There are 2 hotels on the JNB precinct: an IC (expensive) and a City Lodge (cheap). They could presumably arrange tours and would hold your luggage.
So logistically an overnight or day trip into Jo'burg is not onerous. Whether it is worth it... everyone has their own view. Given the prices and timings sketched by the OP I might be inclined to do the overnight in JNB and arrange a tour. The difference in fares would pay for the hotel and the tour. (And since you'll otherwise have to leave for CPT soon after 1.30pm, you won't get much done in Cape Town on Sunday anyway.)