All righty, then!
It would be sweet if the modders used Vercingetorix' tool, but as long as they don't...

would this work?

unzip mod(s) to
rtwdir\mods\modname1
rtwdir\mods\modname2
...
each w/full dir structure

start proggy.
proggy parses mods folder, presents you with list of modnames
You select desired mod from list and click "play with this mod already" button in proggy UI.
proggy checks to see if this is "currentmod", for which it has cunningly stored a value (Hey, it's even pre-selected in the list, ya know!)
If not, it runs first revertToVanilla, then InstallMod.

InstallMod procedure:
parse rtwdir\mods\modname\ w/subfolders.
for each file, check if same file exists relative to rtwdir\
if so back file in rtwdir up to same relative location in rtwdir\mods\vanilla\
if not add filename to mods\modname.uninstall.list
copy file in modname to rtwdir.

revertToVanilla procedure:
find currentmodname.uninstall.list and delete everything mentioned there
Just copy the whole dang vanilla dir into rtwdir