When populating the list of available repositories instead of hardcoding one check for all with exception for particular repository (see https://github.com/moodle/moodle/blob/master/repository/lib.php#L840 ), implement callback in repository class. Overwrite for children if needed.
At the moment repository_coursefiles has it's own check
and also repository_local should also have it's own check - it is not to be shown for the people who don't have 'managefile' capability in at least one course