first make sure the user account in BES has an IT policy with no settings. Then you can delete the account from the BES manager. You can choose to delete all exchange settings as well. This will mean that if the user account is ever reactivated with a blackberry, the saved info like BBM contacts, texts and call log will be gone.
Next step is to go to Options > Advanced options > Service Book
Delete all the entires containing the word ‘Desktop’
You will know have removed the BES configuration from the blackberry without wiping its settings.
Here is a list of desktop service books