Factory reset doesn't function on encrypted devices.
When attempting to perform a factory reset from the version of ClockworkMod distributed on the Replicant site, the reset will fail on encrypted devices, saying that /data cannot be mounted (as ClockworkMod doesn't have the decryption key). When trying to perform a factory reset from Replicant, Replicant reboots into ClockworkMod, which still can't preform the reset. However, when sent over from Replicant, the reset silently fails.
In either of these cases, the correct behavior would be to format the partition instead of trying to mount it and delete its files, but that does not happen.
I don't know if all GT-I9300s have the same partition sizes and layout, but for my device's drive setup, running this was necessary to perform the actual reset:
adb shell mke2fs -t ext4 /dev/block/mmcblk0p12 3022844