Just a follow-up on my original question having made the trip:
I ended up staying at the Radisson Blu Sandton Gautrain Station in Johannesburg for the night in question. (Note that there are two Radisson Blus in Sandton a short distance apart, so make sure you get the Gautrain Station one if you're going to go for this approach.)
I decided to go to Joburg because I had a few restaurants on the to-do list there and hadn't come across anything amazing-sounding to do in Pretoria for the night. And in retrospect it would not have been a good idea to try to walk to the Protea near Pretoria station -- 1.5km is a long walk on the car-oriented streets of South Africa, and it turned out our Blue Train arrival was delayed (as apparently happens often due to various mechanical issues, in our case with the track signals, along the way) so we didn't get to Pretoria until after dark. That said Uber is readily available in the major cities in South Africa so it would have been easy enough to get an Uber over to that hotel, but I don't know if it was close to anywhere worthwhile to go for dinner.
So instead we just hopped on the Gautrain from Pretoria Station to Sandton Station, which took only about 20 minutes (the train goes very fast, actually faster than highway traffic) though it doesn't run very often and stops running on the early side, which is worth keeping in mind and could have been a big headache if the train had been delayed another hour or so later than it was. The Gautrain station at Pretoria was easily accessed though, even with the Blue Train disembarkation being a little chaotic, and the hotel in Sandton was right across the street from the station upon arrival there. There are many other hotels that are fairly close to the Gautrain station in Sandton, but I don't know if I would truly consider any of them walkable, especially with luggage and doubly especially after dark.
At another point in our trip we also stayed at the Hyatt Regency in Rosebank, which was a nicer hotel IMO and also near the relevant Gautrain station, but with the downside that the airport Gautrain, which we took the morning after arriving on the Blue Train, only runs to Sandton so you have to transfer if you are coming from Rosebank, and both lines run fairly infrequently though they are at least somewhat timed for transfers. (There is also a Holiday Inn between the Rosebank station and the Hyatt which would be equally convenient to that station.)
Overall though I actually enjoyed Joburg more than I had in the past -- it seems to be coming into its own, Uber makes it much more accessible than it once was, and the Gautrain is really handy for trips along its route. Marble restaurant was outstanding, in particular. I wouldn't go out of your way to spend time there over other destinations like Cape Town and Kruger during an SA trip, but I wouldn't let the scary stories dissuade you from trying it out for 24-36 hours in transit among other destinations.