When using a custom role which has access to custom forms only, there may be an instance when the Inactive checkbox is disabled in the custom customer form.
To set the Inactive checkbox to True (checked), create a Customer saved search of the entities that will be deactivated and check on the box Available as List View.
Then navigate to Lists > Relationships > Customers > set the View dropdown at the footer to the search you have created above. Set the Inline Editing to OFF and the Show Inactives check box to True.
The Inactive column in the left will be available and the check boxes are enabled. Check on the customers that need to be deactivated then hit Submit button.