To make sure your Veeqo accounts history stays correct you cannot delete a user in Veeqo. The user's account is tied to all their historic actions and removing them would result in these actions being delete.
If your employee no longer requires access to Veeqo we recommend you change the user's password and email address. You can do this by logging in as the Account Owner and heading to Settings>Users. Click onto the user and edit the relevant fields, then hit Save.