If you want to prevent user to doing something you usually can achieve that with (local) group policy objects. You edit LGPOs with Group Policy Editor, but GPOs in fact modify your registry just like you thought.
You can download available Group Policy settings and check if you find those settings you want to disable. Downloadable Excel files also show which registry key will be modified (if I remember right). And those are the registry keys your .NET app will modify.
A word of caution: do NOT test registry modifications in your machine. Get a separate test machine or better yet, use a virtual Win7 machine for testing purposes. A messed up registry is definitely something you don't want to have in your (only) machine :D Good luck!
HTH