Bill - I would suggest an SR on this one. If the agent is physically down, but the OMS does not see it as Down, there might be some other issues or fixes required.
I seem to be having the same problem ..I am trying to delete the agent and it says 'Error:Agent status is UP .Shut down the agent and wait to be makred unreachable before deleting" .
Did you resolve this issue Bill?
try going to target and stopping an agent on the target in $AGENT_HOME/bin/emctl stop agent
or status agent to see if the agent is really running
then retry deleting an agent in OMS12c