ftp.domain.com and the ftp server really have nothing to do with each other. You can remove ftp.domain.com and people will still be able to ftp in using domain.com, www.domain.com, or even the ip address. If you are using some form of domain.com it all resolves to an ip address and that is how the client connects to the server.
It sounds like you want to disable ftp for a certain domain. You cannot disable ftp for a certain domain exactly. You have to disable ftp for the user who has access to that domain.