When you no longer want to host a domain $DOMAIN with HCoop, do the following:
Remove all mentions of $DOMAIN from the files in your ~/.domtool.
Run:
domtool-admin rmdom $DOMAIN
The second step should fail if you haven't been granted permission to configure $DOMAIN. If you finish both steps successfully, then none of the shared HCoop daemons should serve anything related to $DOMAIN anymore.