Can Windows Authentication logins be disabled on SQL Server 2008 (or R2)?
As far as I'm aware it is not possible to disable Windows authentication on SQL Server 2008 + R2:

http://msdn.microsoft.com/en-us/library/ms144284%28v=sql.105%29.aspx

The only Windows accounts that will have access are those that are explicitly added as logins (or are members of a group which has a login).