Even if it would slow the PC down, wouldn't it be feasible to extract all the LGP files into respective folders and run the files from there?
For installing and uninstalling it would be similar to methods used in Oblivion and Morrowind. Keep all the modded LGPs in folders named by the mod title, and as the user wants to install them, extract them into the already extracted core LGP folders.
You would still have comparability issues (similar to ones experienced in the early elder scroll days) but it would be easy to do a clean sweep without reinstalling the game. You could just switch back to the compressed LGP files that would remain untouched.
Another method (and this would be for people with terabyte+ HDDs would be seperate installs or just seperate data file folders. (Data1, Data2, Data3 etc) and running a program like bootleg to create a few different game profiles. then the only hassle would be creating a program that could differentiate between the profiles upon user request (a launcher of sorts). It would be great if there were a launcher similar to skyrim with like 4 options, Start Game, Change Game Profile, Change Music Profile (with cooperation from FF7Music), and maybe an Uninstall or Open FF7 Folder option.
Just some Ideas. I'm not a script writer or anything so Ideas are all I have lol.