To deactivate a user on Apex, please see below steps:
Navigate to Administration -> Security Codes -> Employee Codes.
Select the employee who needs to be deactivated and click on "Change".
Change the Employee type to Past Employees (If no such user group exists then create one under "Employee Type Codes", there should be no rights ticked at all).
Untick the Supervisor rights at the bottom of the page.
Click on "Save".
Please Note
As from Version 2.55 Rev 0215 there is also Employee lockout feature which can be utilised as well.