Is there a safe shutdown command, like a "Halt" for these? Either for web Gui or ssh?
ssh in and use the unix shutdown/reboot command it shuts down all the services.
as for unplugging the network cable and waiting why not just shut down cgminer???
/etc/init.d/cgminer stop
and
/etc/init.d/cgminer start
when u change frequency there is no need to reboot it either just stop cgminer and and start it again.