You could create a crontab job that automatically creates a .tar.gz archive from the subfolders that you want to backup and writes that archive to a directory that is backed up. Run that job a few minutes before automatic backup is scheduled. For example something like:
# tar -czf /backed/up/path/myarchive.tar.gz /excludedpath/subfolder1 /excludedpath/subfolder2
Then you can exclude the whole "excludedpath" path from your backup, yet will still have the content of its subfolders.