I don't use any exes. I just copy the needed paks into the Coop installation. You don't need other than that. To uninstall you just remove the folder.
From the readme:
Return to Castle Wolfenstein: Coop
- Copy all your rtcw pk3 files (mp_*.pk3, sp_*.pk3 and pak0.pk3) inside the main folder of this archive.
- Above is important, don't mix this with your current rtcw installation. You have to play this game as a complete new game.
- Double click rtcwcoop.exe and the game will start.
- You can open the console by pressing shift-escape.
- The source code for this project can be found at: http://code.google.com/p/bzzwolfsp/
If this has nothing to do with Coop. Try returning the files from the trash bin. If not, you can try reg seeker or regcleaner. Also how about giving it a different folder?