I've struggled with same problem for a whole day and found a workaround. There is a special file called "wmpfolders.wmdb" which stored information about all folders looked through by WMP. You can find this file in you local app folder: c:\Users[your name]\AppData\Local\Microsoft\Media Player. What you can do with this file is mark a folder so WMP will ignore it and will not update any files stored in this folder. To do so edit this file with any text editor (it just a plain XML) and replace Exclude="0" with Exclude="-1" to mark folder as excluded.
You can exclude specific subfolders or any top level folder.
Hope it helps someone.