Try the latest beta and let me know how this works for you.
I ended up just allowing a list of folders to be excluded to be specified on the field’s line in the collection template file. For example:
Folder: <folder: excluding: sub 2, sub 3, >
A template line like this would exclude folders named sub 2 or sub 3.
Also, any sub-folders whose names begin with a dot should be automatically excluded.