If you dont need the mail features provided by cpanel, qmail can be installed. The qmail on the server can act as a "remote mail server only" and you can use this server as the mail server for other servers.
I don't think that it would be wise to install qmail on a cPanel server, regardless of whether or not you configure cPanel to use any email accounts. Whenever cPanel decides that a new version of exim needs to be installed, it will overwrite certain files that are used by qmail (e.g., the path to the sendmail binary), and will attempt to configure exim to run on bootup (which, depending on the startup order of your scripts, may cause qmail to not start properly). You will be asking for a lot of trouble if you try to mix the two.