Instance admins should be able to disable the "Custom CSS" option for users. This should probably accompany T563: Instance-level stylesheet.
Suggested on the forum:
Option to limit user customizations. One of the things I actually liked about Medium was how little a user could do other than write. If I can’t disallow user customizations entirely (which is fine), I’d like to be able to restrict or minimize the options available. When a reader visits my instance, I want them to know from looking at it.
Add a new instance-level configuration option.