Had the same problem. My wifes messages sent from her iPhone had my name as the sender. If one of you can function without your @me.com email address (which she could) I think I have a solution.
On your wifes phone turn off Mail (under: Settings, iCloud). She can still use any other email service.
Make sure your name appears as the user in which ever service you use. Same for her. Some you can change from the iPhone in the POP Account Information (under Settings, Mail Contacts Calanders, Account) others on line, such as iCloud here:https://appleid.apple.com/cgi-bin/WebObjects/MyAppleId.woa/
Hope I got the link right, first time using forum.