Mechanics whose purpose is to purely hurt your opponent without benefiting you are very rarely used by human players (see damage-your-enemies-cities spells in MoM, like Famine or Corruption).
In general, my 2c is that these "humanitarian" ideas like "make the world righteously outraged at you for sniping an independent city" are misguided in a civ-like game and aren't really a better representation of reality than what we have now. Civ isn't really
that unhistorical at imitating diplomatic relations, although it's obviously nothing like history at all when it comes to internal management - and international diplomacy is, and has always been, a dog-eat-dog world in an even higher degree than internal politics.
Historical things like minor confrontations between two civs blowing into world wars due to power plays and webs of alliances already happen quite often due to the "world wars" mechanics. In my Mughal game, this action of mine
resulted in a massive world war though a web of alliances, a war that resulted in large-scale conquests by all civs involved (that didn't include me). Ottomans kicked Arabia out of Asia at all, leaving the Arabs to their South American and African possessions, but Germany and the USSR attacked Turkey in defence of Arabia, with Germany conquering Constantinople and making a blitzkrieg though the Middle East, while USSR took Caucasus and invaded Iran.
The only reason such wars don't happen regarding independent cities is because you can't communicate with them in any way, not because other civs aren't prone to moralistic outrage. I'm not sure, however, that allowing alliances/loose vassalization of independent cities is a good gameplay idea, and it would likely be hard to implement as well. And it will likely result in even more wars all over the place.
Although I never sign defensive pacts, both in Vanilla Civ and in RFC derivatives, anyway.