USB wasn't designed for this use case, and it is a very, very common problem.
Certainly, UBS in general can't be used for this purpose, but if there's true industry buy-in for MIDI over USB then it's not hard to imagine more and more USB hardware will get made that can compensate for that problem. For instance, I wouldn't imagine laptops to get isolated USB, but a shiny new post-MIDI-2 audio interface sure would.
In that environment, isolation is a constant concern. Connections that are inherently isolated make fault-finding far more straightforward and obviate the need for external isolation boxes.
For even a simple USB audio interface setup connected to a single audio source I would recommend isolation and balanced audio cables.