StringingTerror

First you open up Mod Organizer and go to it's settings, In one of the tabs there you uncheck the Associate With Nexus box. After that all you have to do is uninstall. (NOT SURE IF THIS HELPS)You could delete it but to be sure there are no unused extensions left you should run a program like CC cleaner. Though in this case I think everything is in the installation folder. Afterwards you could delete the cache from your Browser if you want to be 100 percent sure. thats how I did it.

This is really late but if anyone from google sees this. You have to Load the Skyrim.esm(by itself) first then load the other master file( In this case it's race compatability).