@hechla I have continued to make tweaks to our settings since posting this and some of the newer features (such as limiting registration to a domain) may take care of the some of the things I did with scripting.
With CSS, we hid all of the registering form stuff so that did not show at all to our faculty/staff (happy to share our scripts)
With JS, we put a warning message about this course being just for our Faculty and Staff and directed people to login before trying to click enroll. We did the same thing on the registration page if they got to that without logging in.
Again, there are now probably better ways to set this up since we did a few years ago but it still works well for us. It has completely stopped all the duplicate accounts people were making by creating new versions of themselves to take the classes we asked them to take.
Hope this helps!
Nick