I don't have a copy of PerlDesk 1.7, so I'm not sure if this would work, but did you try changing the group ownership to shared?
chgrp shared /home/e-smith/files/ibays/networkhelp/cgi-bin/email.cgi
Also, where are you piping the message? is it from a user .qmail file? Have you tried using the email.cgi outside of qmail? (ie take a message in the Maildir and do something like:
cat message | /home/e-smith/files/ibays/networkhelp/cgi-bin/email.cgi
Does this work?