Haven't tried it (and don't use docker), so a wild shot: https://github.com/jupyterhub/repo2docker
'repo2docker fetches a repository (from GitHub, GitLab, Zenodo, Figshare, Dataverse installations, a Git repository or a local directory) and builds a container image in which the code can be executed. The image build process is based on the configuration files found in the repository.'
That way you can perhaps just delete the docker image and everything is gone. Doesn't seem to depend on jupyter..