I have ran into this same issue. There is an additional email address field in Service Desk called 'Email Address 2'. This field is checked when the email is being processed by the Inbound Mail service. If you are not mapping AD to this field, you can set their correct email address in this field and it will not be overwritten. This field is not used for notifications to the users, it appears to only be used by the Inbound Mail Service. If you do have another source for the users actual email address, you can setup a data import to populate this field automatically.
Jonathan | Lead ITSM Consultant | Network Consulting Services, inc. | Desktop, Network & Internet Security
I will try that Thank You!