In order of likely to work, but risk irritating people:
1) You can delete everyone's local config.pro, which may not make everyone happy as it will also take out the customization. This can be done with software deployment tools.
2) You can move everyone's local config.pro to a new name and let those who like what they had copy the pieces they want to keep. This can be done with software deployment tools.
3) Edit each local config.pro and comment out all the mapkeys or cut all the mapkeys and paste them to a new file. This is more difficult as scripting is involved, but the mapkeys are identifiable with ordinary text editting techniques. It can probably be done with software deployment tools.
4) Generate a list of the new mapkeys for the users and let the users sort them out. This works best if they have some understanding of how mapkeys get appended to their local config.pro without their realizing they are sometimes copies of the loadpoint mapkeys.
Depending on the users and the level of work-environment rigidity any of these is a possibility.
Keeping the majority of the mapkeys out of the config.pro file is a good idea. They can stay in a text file and get loaded with the only mapkey that needs to be in the config.pro (or manually if you like) which keeps the config.pro file orderly and lets the mapkeys get easily editted using Notepad or the like. Being independent one can have several sets of mapkeys dedicated for particular jobs.