The System Permissions assigned to standard profiles are not editable. If you need to edit them, instead, clone the profile and make the changes there. Then, assign your users to the cloned profile rather than the original.
On a Custom copy of the System Administrator profile, it's fine to disable that permission - although note that the other permissions given to that profile mean that any user can trivially put it back. System Administrator rights are and are intended to be the keys to the kingdom; if you don't completely trust a user, do not provide them with that level of permission.