I'm pretty sure the RTW engine allows you to simply target your own agents/FM just like you would an enemy one. I think this was changed in MTW2 so that its not an option anymore. So as far as I remember, (dont have EB on my comp at the moment) you can assassinate any of those disloyal or incompetent generals you want. If not you can always put them on a boat and crash it into some Illyrian pirates.