How can I use the /home directory on Mac OS X : revisited
Personally I'm convinced that any software requiring hard coded paths to home directories is broken and needs to be fixed, but I understand that this isn't possible sometimes. So in your situation I would just disable the auto mounter for /home (see How to remove '/home' directory?) and then symlink /home to /Users. This also solves the backup issue.
PS: Biggest risk probably is that a future update will rewrite auto_master but that you can easily fix again.