Setting up a vm is the safest and most flexible option.
The fp-lib-table is not the real problematic setup file. Nightly can use the libs that are used by stable. (The other way round is not possible.) There are other setup files that might create problems. (One per application) These are in the same folder as the global fp-lib-table.
At least in linux these setup files are in a user specific folder so you could simply have a user specific for nightly and one for stable.
Another option would be to have a startup script that copies around your setup files.
Or you find a portable build version of the stable release that has it's setup files in a different folder than the default location for kicad. (I doubt there is such a portable version for nightly.)
The last option would be to change the locations of these files in the sourcecode and compile kicad your self.