This frustrated our installation as well. We ended up changing everyone's userPrincipalName in Active Directory so it matched their e-mail. Microsoft's Scripting Guys have a nice article on that -
Hey, Scripting Guy! Blog : How Can I Assign a New UPN to All My Users?. That worked for us, but may not be an option for all people.
I agree that we as the end-user should be able to choose which AD attribute that should map to the e-mail address field in Shoretel. For example, AD has an attribute called "mail". That would be the perfect one for use for us.
I really hope Shoretel improves their approach to active directory integration. It does work, but it seems like it was added without a lot of testing or thought.