Well I want to extract the messages from the user's POP3 box using a PHP script (should be possible) and display them in my mail interface the web site...like hotmail but with no option to get mail in a mail client. Sorry for being a little unclear...
Well you could still change the port and the tell webmail what port it is, someone could find it.
Second you could disable pop/imap and go with a webmail client that doesn't use either and pulls it from the mail dir, mbox. I think horde might work this way, but I am not sure.
Another thing you could do is have their imap username be something funky, then use a squirrel mail plugin http://www.squirrelmail.org/plugin_view.php?id=37 that allows you to give them an alias username that would allow that username to login to SM, but not a pop/imap.
For every server, you can configure on what devices it should listen!
E.g. if you use xinetd for POP3/IMAP, tell it only to user localhost (127.0.0.1) for these services.
You are also able to restrict a service to be accessed from a list of hosts (xinetd, inetd, iptables,ipfadm) ...