I think it would be great to add a core configuraiton option for the host to optionally turn off duplicate usernames across portals. This can be done in DotNetNuke.Entities.Users.UserController in the AddUser method where there is explicit code to support thes shared user identities.

In the AddUser method, if the user already exists there is special logic to allow the often unwanted SSO. I simply commented out this code in my implementation and returned UsernameAlreadyExists. (this code is based on DNN 3.2.2).

                ' check if username exists in database for any portal
                Dim objVerifyUser As UserInfo = GetUserByUsername(Null.NullInteger, objUser.Membership.Username)
                If Not objVerifyUser Is Nothing Then
                    If objVerifyUser.IsSuperUser Then
                        ' the username belongs to an existing super user
                        Status = UserRegistrationStatus.UserAlreadyRegistered
                    Else
                        ' the username exists so we should now verify the password

                        Common.Globals.SetApplicationName(objVerifyUser.PortalID)
                        '                        If AspNetSecurity.Membership.ValidateUser(objUser.Membership.Username, objUser.Membership.Password) Then
                        '                        ' the specified password matches the password on file
                        '                        UserId = objVerifyUser.UserID
                        '
                        '                        ' check if user exists for the portal specified
                        '                        objVerifyUser = GetUserByUsername(objUser.PortalID, objUser.Membership.Username)
                        '                        If Not objVerifyUser Is Nothing Then
                        '                        ' the user is already registered for this portal
                        '                        Status = UserRegistrationStatus.UserAlreadyRegistered
                        '                        Else
                        '                            ' the user does not exist in this portal - add them
                        '                            Status = UserRegistrationStatus.AddUser
                        '                        End If
                        '                        Else
                        '                           ' not the same person - prevent registration
                        '                           Status = UserRegistrationStatus.UsernameAlreadyExists
                        '                       End If
                        Status = UserRegistrationStatus.UsernameAlreadyExists