Currently persist.sh is limited to saving and restoring files. I suggest modifying the script to permit it to save and restore directories in /etc as well. My specific need is to save and restore /etc/init.d and the files therein (I have some things I need to run at boot, including, for instance, crond).
This could be as simple as adding -R to the cp commands, though it might be worthwhile to add a -P flag to specifically preclude dereferencing symlinks (to avoid filesystem loops).