If I may add something here
In my opinion, something should be done with:
1) "You took to many cities comparing to the total urbanization of the world". This maybe makes sense if in modern era Adolf Hitler captures 20 cities out of 200 cities in the world (by the way, I very rarely see 20+ city empires, and I have never seen empire bigger than 28 cities American madness) because that means true total war and massive warmongering over continents. If somebody conquers 20 cities, he is true warmonger and true danger to the entire world - also, all civs can see that in the modern times.
But I don't think 20/200 cities in the modern times are equal to the 3/30 cities in the ancient times, somewhere in the deep jungle when nobody knew about the war. Conquering 20 cities is total war, conquering two cities is simply only possible solution if Hiawatha is near

but the warmonger mechanism views them as exactly the same thing.
Though I have no idea how to balance that.
2) "You took the last city of a civilisation!"
To be honest, this idea seems so silly for me, that I would love to completely delete it. It makes no historical and gameplay sense - let's imagine giant terrifying war, in which the entire empire is massacred, nuked, pillaged, loses capital and stays with one city somewhere far away - currently the civ thich would take that one city, can receive bigger penalties than all those warmongers which destroyed the entire empire. Why? Because that was the last city.
And?...
If big power falls and is destroyd by other rising power who is bigger threat to the stability - that rising power which captures 10 cities, or one little poor state, which takes one last city of the fallen empire?
3) "You took the city state!"
Rule 2) makes war with city - states impossible, that messes with a balance... When Hitler was regarded as bigger threat - when he took "city state" Austria, or when he took Capital of the French Empire? This game would regard conquering half of Europe as little penalty, while conquering Vienna - extreme penalty.