Humm, I haven't done it for a while so I wasn't sure..
It's entirely possible that because you're botting into an emergency maintenance mode, the filesystem is still read-only.
Try issuing:
/bin/mount -oremount,rw -L/ /
This should remount your root filesystem in read-write mode. You should then be able to modify /etc/modules.conf freely.
One long-haired git at your service...