They could put in a passive mode or something which only allows you to kill rogues but not other agents. This would help with those situations where you hit someone by accident due to cross fire.
Have the downside that you can't become rogue unless you disable the option but have to wait a certain amount of time before you can kill anyone.
I just think they need a better way to discern intention. Some way to figure out that 90% of my damage just went into AI so clearly that grenade wasn't intended for the agent the went all Leroy Jenkins.
That or if you go rogue with a 20 second timer you should be able to immediately give yourself up, drop one item and a little XP, reduce the sentence.