What about a terminal based security configuration wizard that could be launched by the user after the install finishes? I don't know if any current solutions exist that would allow a novice to easily configure security-groups and firewall/iptables after an install completes. I think if you combine some of the most common hardening tasks into an easy to use script with some default templates, it could make things a bit simpler. Hopefully this would eliminating some of the reasons folks just disable the security features. I think the SELinux troubleshooter has helped accomplish the same thing for desktop installs.
Wilbur