There was a patch applied to /etc/hotplug/net.agent that autoloaded network interfaces when they were plugged in. The problem is that I don't want my eth0 card brought up even though it exists. That's the reason I have an ! in front of it in my /etc/rc.conf.

There are a couple of suggestions:
1) get rid of it -- /etc/rc.d/network handles all network interface loading (doesn't work so well for people with pcmcia cards).
2) change /etc/rc.d/network to not ifup anything that's not enabled in INTERFACES -- why run /etc/rc.d/network ifup then, if it'll all be loaded by an /etc/rc.d/network start? the only "benefits" you get by loading it with ifup are no route and the network script not being marked as running. I don't see these as benefits.
3) let the user choose if they want hotplug to ifup interfaces. a variable in a script in /etc/conf.d would say yes or no -- this would probably work for most people, though some people might only want to bring up certain interfaces (like pcmcia ones)
4) let the user choose which interfaces hotplug will ifup automatically -- either in /etc/conf.d or /etc/rc.conf. Then the people that do want this functionality can just enable it (or the people who don't want it can disable it). The only problem then is that routes don't come up when their related interfaces do.