If you install either KISS or APF you may safely remove the contents of /etc/sysconfig/iptables.
With the KISS script you really don't have to; the first thing it does is clears anything currently in iptables, before it installs it's own settings.
I'm not sure, but I'd think that APF would do the same thing; it's the only way to get to a known state.
Using chkconfig to shut off iptables will cause the system to NOT set up the settings in /etc/sysconfig/iptables, but it won't keep KISS or APF from running and making changes to the firewall.
Jeff