I tested installing BOINC, running Rosetta@home, and Folding@home together on the same machine. Rosetta@home currently only uses the CPU, not the GPU. Rosetta@home has not had the influx that Folding@home has had, so it is currently assigning WUs reliably. This means that when Folding@home has not assigned WUs the CPU, at least, is not idle and is doing work for Rosetta@home.
I set Folding@home to run at a slightly higher priority (Configure > Advanced > Folding Core Priority > Slightly higher). When it downloads a WU for the GPU there's really no impact and it computes as fast as it did before. When it downloads a WU for the CPU it is using around 60-70% of the cores and computes slightly slower than it would otherwise, but it's still quite quick.
I also experimented with BOINC's 'suspend when CPU activity above X%' setting, but actually found this to be unreliable so just left it to compute all the time. Rosetta@home and Folding@home are sharing quite happily.
In setting it up this way, I found I am less inclined to try to force Folding@home to download WUs since the PC is now always being productive for an important cause.

P.S. Once again, a huge thank you to the team for dealing with this influx and letting us mere mortals help out, and a huge thank you to the volunteers on the forum for answering all of our questions.