In doubt, abort the mission. If you do, the negative score will be of the amount of civilians that died. If you don't, it will be that, minus the amount of soldiers you lost, plus the amount of aliens you killed, amount of artifacts recovered, and amount of corpses/captures.
In my experience, unless you can assure you will bring most of your boys and girls back to the base (tier 2 weaponry, armor, etc), it is better to abort. You will more often than not recover the score on salvage and ground assault missions, even with the country that had the terror mission.