Seems odd that the kill switch for the onboard card would turn off the USB card too, but anyway.
I suppose you could blacklist the driver for the intel card. Add a line to /etc/modprobe.d/blacklist.conf
reading blacklist iwlagn
. You can do so as follows
echo "blacklist iwlagn" >> /etc/modprobe.d/blacklist.conf
That should prevent it from loading at boot. Make sure you use two >>, just one and you'll overwrite the file.
Check that it's not loading when you reboot
/sbin/lsmod | grep iwl
No output means it isn't there.