http://download.microsoft.com/download/6/B/3/6B33690B-E742-42A9-AB1C-F9146A70917B/MSIA_User_Guide.docYou can create a custom file to be passed at command prompt to the msia. If your OU's are based on sites/IP addresses, you can always specify the same in the custom file.
However doing it on an OU is not possible. The alternative way is already known to you.