Just like the MS 'home' directories, Microsoft's 'best practices' states that you should share out the 'home' folder, then protect all the individual subfolders belonging to users with NTFS permissions.
You would share out \servername\home
Each subfolder would be setup such that each user had RW access and that's it.
I would guess you have a similiar structure for your documents folders. You could use the same 'best practice' guide and have sharepoint mount the \servername\documents\ folder for everyone. Sure, everyone would have to find their names in the list to get to their documents, but it solves your sharepoint issue immediately.