chkconfig merely manipulates the files and symlinks located in /etc/init.d and /etc/rc[0-6].d folders (well and sometimes /etc/xinet.d/stuff). You'll have to check in /etc/init.d to see what script corresponds to httpd. Likely you'll want to make sure your custom init script is called "httpd-custom" or something and then configure it separately. Configure httpd to be off all the time and httpd-custom to be on at the appropriate runlevel.
Thanks to the help of the amazing Jared Smith, I figured out the problem. When yum ran, the new httpd rpm renamed my custom init script to httpd.rpmsave and wrote out a new standard one as httpd. So, after changing httpd to httpd.stock and httpd.rpmsave to httpd, everything is back to normal.
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