I do very little with ftp but I think you just need to remove it's entry in the /etc/inetd.conf file and replace it with an entry for your new program. If your running it as a daemon instead of through inetd, you can just remove the startup script from /etc/rc.d/rc3.d/ and any of the other run level directories under rc.d.
I believe that should do what you need.
Good luck,
GJ