The next patch for Civilization VI will make conquest a little less painful. The Spring 2017 update, features tweaks to harbor bonuses, combat unit strength, and finally adjusts penalties for warmongering so that the political game hopefully won’t seem as capricious. On the diplomatic side, Firaxis has reduced the warmonger penalty for declaring war or capturing a city based on your existing relationship with that other civilization. Players will now get less of a penalty if they are already denounced, and much less if they are at war.
Macedon is at war with Persia. If India goes to war with Persia sometime in the middle of this Macedonian/Persian War and captures a Persian city, Macedon will reduce its warmonger penalty against India by 40%.
The developers are also reducing warmonger penalties for city population after a city capture if the city is smaller than the average city in the game.
Persepolis is conquered and its population after conquest is 6. But the average size of a city in the game is 8. So this city is 2 / 8 = 25% below the size of the average city in the game. Therefore the warmonger penalty is reduced by 25%.
The Spring 2017 update is scheduled for later this week. Just in time for the Double Civilization & Scenario Pack featuring Persia and Macedon.