The following dockerfile is working for me right now:
FROM suse/sles12sp2:latest
ADD http://smt-server-fqdn/smt.crt /etc/pki/trust/anchors/smt.crt
RUN update-ca-certificates && zypper --gpg-auto-import-keys --non-interactive patch --no-recommends --with-interactive --auto-agree-with-licenses; zypper --non-interactive update --no-recommends --with-interactive --auto-agree-with-licenses && zypper -n install --no-recommends apache2 apache2-example-pages && zypper clean && rm -rf /var/cache/zypp*
As you can see patch, update, install and clean are working, refresh does not. But please dont ask me details about all this.
The system was registered against our SMT server before we integrated it with SUSE Manager. Maybe there are essential parts left which make zypper working inside the container.