If you are notified that a user has left an organisation there are a few steps to disable them in the system.
It is best practice to not delete them as any history associated with them will be lost.
Open the contact from the CRM that you wish to disable
Click on the Edit button (top left) to edit the user
Click on the 'De-activate' button
Enter some characters in front of their email and 'Save Draft' to ensure no emails are sent to them
You can then contact the organisation and get them to update the primary contact on any active applications.
Alternatively you can change the primary contact.