The points don't have to be bought they can be earned from creating content etc ( so they are free that way ), You don't have to offer them points via a stand alone commerce package either, then they have no actual moneys worth, I would also say if you offered them x amount of points free when they upgrade their usergroup etc then they still have no actual value, they purchased the membership upgrade not the points.
You would need to disable the shop and just use the points earning system from it, the shop has lots of permissions for user groups each item so you could only allow x user groups to buy x item/s etc.