Recursive delete of a directory is not something the RFC
mandates servers implement. (Not very surprising if you
look at the system call, rmdir(2) doesn't delete
non-empty directories). If you insist on doing this via FTP,
you have two options:
Clean up the directories yourself by having the client
traverse the directories, and deleting files.
Find, write or modify an FTP server that will support
this feature. You might have to modify Net::FTP
for that as well.