Killing all of them and taking the bodies elsewhere, far away from the village, would be a smart choice. Leave some fake traces suggesting the group never made it anywhere near the elven village before getting ambushed. The fortress commander ought to believe easily enough the ambush was performed by the same unknown human who raided the fortress earlier. This way he might, again, spend time hesitating before bothering the elves again, plus he wouldn't have a reason to believe the elves are any more dangerous than they have ever been.