Well, you can prevent bypassing the mail server to send mail, and block users to create spam scripts by enabling the SMTP Restrictions. Enabling the SMTP Restrictions will prevent users from bypassing the mail server to send mail. Once enabled, it only allows mail delivery through MTA, mailman, and root connect to remote SMTP servers.
Note: This method will work for the root users only.
Enabling the SMTP Restrictions
Log into WHM as a root.
Type smtp in the search box, and click over the SMTP Restrictions from the result.
Simply hit the Enable button to turn on the SMTP Restrictions.
You can easily Enable and Disable SMTP Restrictions from the same window.