So after half-fixing the problem, I rebooted into CWM-recovery (from CF-Root, like I said), and had a look at /system--it's totally erased. /data looks pretty bare, too. I think everyone without backups will be screwed...
Also note that CWM-recovery from CF-Root only detects external storage on my phone. But if your backups are on internal storage, I'm sure you could trick the system and mount it in place of /sdcard.
What concerns me even more is that I can't boot the supposedly stable version of ClockworkMod Touch Recovery that's linked in the first post. Only the CF-Root version.