This should be raised in the The Three Kingdoms mod part of the forum (if there is one).
The way to keep your orginal R:TW install clean is to simply take a copy of it and then install any mod onto a copy of the original install. So, if a mod messes up the game then you still have a working copy of your R:TW install.
If you uninstall R:TW you will be able to re-use your CD-Key. The CD-Key is only required when playing MP games.
The following is an old screen shot that shows I had 11 copies of the R:TW install: