writing the script to log email addresses could be reasonably easy. If all of these users are going to have an account on this server anyways, you could simply create a box that lets you add a username, and have that entered into the linux box via pushing that command to the operating system. Then, before entering the username into the database you could simply append "@yourserver.com"
; to the username, and presto you are still using email addresses as the primary key. The way to keep passwords synchornized could be a bit difficult, especially if you are using encrypted passwords. If you are just using plain text passwords on your system it would be much easier. Sadly this is a reasonably huge security hole if you have people telneting or sshing into your system... if you only want user accounts on your system in order to create email or samba accounts this is another matter... in this case only administrators would need shell access.