That's indeed a bad idea. etckeeper creates a local repository in a protected .git directory inside /etc, don't confuse git with github or other hosting services. I use etckeeper on various machines, just to track changes in configuration files (both those caused by people and package updates). On top of that I use a conventional encrypted backup solution. I never push or pull the git repo anywhere, and I think that's the normal way of working with etckeeper.