There are no basic tools to achieve your business task. Even if you remove all employees role from the users list of role, he or she will still have it on the database level. This logic can only be changed with the development tools but we would not recommend to do it since there are a lot of application functions associated with All employees role. Removing it from the users might lead to inappropriate application performance.
You can try to update the default All employees role id associated with the user.For example, as you see the user doesn't have any roles selected http://prntscr.com/q26wjn, however she still has All employees on the database level. You would need to update the sysadminunitroleid with the id of required role http://prntscr.com/q26ywo instead of All employees role id. I do not guarantee that it would help you to achieve your business task since we do not have any examples of any similar changes in the default roles logic.