The only reason I can think of is the liberation bonus. You're correct, Civ5 does not have war weariness, instead it has an incredibly fragile diplomatic system, and warmonger penalties can weigh very heavily. There can be a tertiary civ that you have all positive diplomatic bonuses with, have a DoF and seems like they'll be your BFF. Then you get hit with a warmongerer penalty and that heavy, heavy positive diplomatic status swings past good and straight to neutral. Then some other civs that they like chain-denounce you and suddenly your friend is one of your many foes.
If a city has been taken by another civ that you're at war with and you conquer that city, you have the option of liberating it instead of burning, annexing, or puppeting. This gives control back to the original owner of the city (a loss, but often you don't want the city anyway, it would just weigh you down.) A great thing to do when you're at war with someone who conquers a city state, because you not only get the diplomatic boost but also 150 influence. By opting to liberate, you not only don't add to your warmongerer score with other civs, you subtract from it.
So liberating is a way to warmonger and still maintain some positive diplomatic relationships. BUT, you cannot liberate a city if you were at war with the civ at the time they were eliminated. Whether or not you were the one who captured their last city doesn't matter, just whether or not you were at war with them when they were killed off. And while you don't plan on removing them from the game, a third civ may DoW them and finish off their last city (that you've been bombarding, so it's health is low/zero) on the same turn, which prevents you from ever liberating any of their cities.