The MigrationWizard's object picker/query builder will work with Exchange 5.x. The object picker you are using is the IDsObjectPicker
(see msdn docs for more info). The problem is that the attributes we are looking for are not supported by Exchange 5.x. Thus our code treats the user records as invalid and doesn't add them to the set of users to migrate.
We have support for Exchange 5.x in our roadmap.... it's coming!