Go to Course administration screen. Locate the button to add students to course. Click and search for the user, select the user and add to the course. The user also gets notified when he is added to the course.
In version 4, you no longer need to remove the menus using code. You can simply remove the Buddypress menu items from Appearance > Menus > Profile Menus or the other option is to create a different Profile Menu for a different user role