What research and intellectuals though, especially in the ancient era? What refugees are going to make it across landmasses when boats have barely been invented? How many atrocities have been covered up to this very day through propaganda?
I mean it was not until recently that we realized that the Neanderthals were not just savages, and it is very likely we killed them off.
History is written by the victors, after all.
Oh, and what about the Barbarians you wipe out too? If you think about it, there's little difference between the civ you wipe out in 2000 BC and those guys too.
You mean, there is no oral traditions recovered in the works of ancient historians?, there is no way to get a little glimpse about what is Greek's opinion of war by being told about the Ilyad?, that the warmonger picture we have of Monty is not because the Spanish reported, when reaching Aztec lands, several minor populations were willing to "use" them (or willing to be "used", depending on how you see it), to overthrow him - they couldn't be considered a "living civ" at that time, considering Civ Scale (refugees do not need to cross seas - as said before, you just find them "hidding" in zones of your landmass your civ "blob" does not cover still (or -in minor percentage-, even inside it). Maybe enslaved populations of different ethnicity or language came from nowere?. And, as comented in my last sentence, propaganda may be a counter, but it is still not implemented in game, and has to be effective (and, If we know there has been propaganda, is because we revealed the truth from other hints, or because there has been counter-propaganda"
We did not know about neanderthals because we did not care about them, or about the tribe confronting them, because we are not relating to either (Neanderthals are gone, Sapiens are we, so we don't see us as "other people" we need to underestand). Of course, our interpretation of what happened will not be 100% accurate... but neither is when they see decide on your warmongering because of just 4-5 standard types of casus belli.
And last this:
"You occupy a foreign capital. I believe everyone can know this by looking at the Domination victory screen."]
Now that, I think I'm willing to settle for.
Though this is accounted for via "we are winning" if you own enough capitals.
So, they can't know you wiped a civ because you are under the FoW, but they have a "magical mirror" that tells them you occupy a foreign capitol (How do they know this city was not founded by you in first place?... because the great god UI exists, I think...
That leads me to:
When we are talking about realism?. Are we talking about it in game terms or in history simulation terms?.
If it is "the computer hacks the rules" I might underestand (tough I argue the "warmonger" counter for each civ should be available in the UI - and i think it is not because, 1) nevertheless, we don't care, and 2) we know already who are the warmonger civs.
If it is "history simulation", we enter the ... "we have o10,000 square kilometers area cities" discussion... you cannot claim nobody else has seen you because there were only you and Peter. There can be much more "minor" people not worth representing in the game because they are not relevant to the major game. You cannot confirm that none of the russian "tribes" has survived (even within you people) passing out traditions on how they were a free people and then were butchered by the current rulers (Bible comes to mind, don't know why...

). Of course you don't "see" them in the game board or the city screen because they are irrelevant on the "scale" you are playing, but there can be hints of them somewere, and the fact other civs know about your warmongering is one of these hints.
Realism and gameplay must be balanced out. The poster talking about Option A and Option B explained well why Option B makes most gameplay sense, and the game symbolic nature is the reson why you cannot discard Option B as unrealistic. (As commented, Option B it is as Unrealistic as a polder covering the full bay of biscay, and we are more or less fine with this second).
Ah... and barbarians do not grant you warmongering because its symbolism (camps instead of cities) means they have not an organized nor a common view of themselves as a "disctintive" group of people... so they are not going to mourn the loss of their status if conquered.