There really needs to be a way to reset /etc to the default (except for a few files like fstab, passwd, and shadow). A good way to detect what needs to be reset is using the command sudo ostree admin config-diff which lists what has been deleted, modified, or added to /etc. The reset function should make a new deployment with the reset /etc. There could be a bash script or possibly a python script that does the function called reset-etc in /usr/sbin which needs to be ran by sudo. It could also be activated by ujust reset-etc which would run sudo reset-etc.
This script probably should get its own repo too possibly if needed