For anyone landing here from search engines, I was able to solve this error by linking supervisor.conf to /etc/supervisor/conf.d/frappe-bench.conf
cd frappe-bench
sudo ln -s `pwd`/config/supervisor.conf /etc/supervisor/conf.d/frappe-bench.conf
sudo service supervisor restart
bench setup socketio
bench setup supervisor
bench setup redis
sudo supervisorctl reload
Now bench restart should work without issue.