Hmmmm. Maybe I open a second connection to the server and check in a loop to see if the directory still exists or is gone. That "should" (watch the weasel word) keep the original connection from terminating.
Comment on Re^2: Need Net::FTP rmdir time out help
Or perhaps run (via rsh) a script to handle the deletes? It could use a semaphore file to indicate it is still running. Your other process could check for the presence of that file at intervals and continue once it has disappeared.
But God demonstrates His own love toward us, in that while we were yet sinners, Christ died for us. Romans 5:8 (NASB)