First to start with a disclaimer. I am quite new to wargaming, and have not played a lot of games. So probably I will overlook a lot of rules and concepts. But I will try to write some summary I could find right now.
In general wargames don’t bother to much with civilians. I have read a couple of recent wargames battle reports and most did not feature any civilians. When they do participate I could identify a couple of reasons:
Think about farmers defending their crops against raiding and stealing cattle. Most of the time not part of any team, but acting like some kind of military units with low capabilities. The actual live and living of these civilians is most of the time not considerd, and wont have impact on the story or campaign. This is mostly used in medieval or more ancient battles and sometimes in fantasy or sci-fi adventures.
( Negative or Positive) modifier
It is not good to have civilian casualties, but they are only some negative modifier to the end score. Often seen in ww2 air war games, were you try to recreate bombing of a city, were missed bombs (which have civilian causalities) generate negative points. But is might also be used in modern urban warfare. But it might also be used impacting morale, as the civilians are liking your side more or less.
Those refugee streams can clog up roads, or make moving around more difficult. It just act the same way as terrain feature, impacting your military forces. They might be moving around as a walking forest is which you only see in fantasy setting, so refugees make up a more believable story, in historical setting.
Unexpected military unit
This is mostly used in modern irregular wars, were mobs of civilians are either blocking your road, or suddenly turning back on you and showing itself as military unit.
Starting the research I had expected that there would be not much ways to involve civilians in wargames, but multiple different ways have been discovered. The only one missing, which would make sense from human rights perspective, is a direct head on head wargame, civilians against a militairy power, where the civilians do not use weapons, but score by avoiding casualties. I haven’t found a system what uses these kind of mechanics yet. Maybe I have to create my own.
Now looking back at the original question:
Can wargame rules include human rights violations, and still teach us a lesson, while telling the (his)story?
I don’t think the mechanisms above tells something about human rights violations. They do take civilians in account, and can create good (his)stories. But don’t teach us about human rights violations.
For this I have to search futher or create my own. From computer games I want to highlight two examples, which takes some civilian live into account. The first is “This war of mine”, which is a game where you play as civilian in a warzone, and try to survive in your house. You are searching for supplies and encounter thereby other people, were you can steal their supplies or fight them. The emotional aspect has some place here, as it feels not good to steal from an elderly couple. But if you don’t get the supply, one of your characters die. The second game is “Conflict Zone” were two parties battle, but the resources are civilians. For the “good” side, you try to save as many refugees as possible, for the “bad” side, you don’t care, but need to indoctrinate as many civilians as possible.
Maybe these games can be a good inspiration for finding a solution. Hope to expand this research in the future.