as to my earlier suggestion with the diplomatic mission... here's a little hypothetical (and it's a tad over simplified, i know)
lets say this later mission has 3 potential outcomes. the first layout depends on you being honest, either you destroyed the facility, or you made the deal. but you never reneged.
so lets say you're in a room full of kett, there's a kett officer who survived the exaltation base, and he's in command of the opposing force. you have work to do, they have their jobs as well, time is an issue for both. you both back down and avoid a fight. or you can duke it out... and they withdraw after a short fight. and you don't waste too much time, and you arrive in a timely manner and save the day. (that's the first 2)
with the last, the kett officer remembers you opens fire without the option for dialogue, and instead of withdrawing he digs in his heals, and you're forced to fight an enraged enemy force to the death, as a result you took to long and there's heavy friendly casualties, and hostiles are more numerous, and with more foes of higher caliber.