I strongly recommend that you put a Java SSH client on your website, as only SSH will offer the kind of security that you need. I know many universities and organizations that use them. It is really convenient (and secure) for the students; they only need a browser with Java to have it work. You should check out one of these:
*
MindTerm (free for personal use)
*
JavaSSH
Also, for email, there are many good free webmail programs that you can use.