Thinking on how horrific events like the Rape of Nanking were makes me wonder if it's even worth doing anything about nukes is we're not going to make Razing cities have MASSIVE diplomatic hits at later eras.
This is where gameplay mechanics differ from real life. Real Life we can argue the moral loss with X event.
But in gameplay terms, a razing occurs because the opponent has already lost. You took the city, you do what you wish to it. Razing doesn't help the warmonger win more per say, it just helps clean up the mess.
Nukes:
1) Can destroy an entire army in a single stroke
2) Can do a mass pillage and make the conditions unusable without cleanup.
3) Can immediately wreck the population and infrastructure of major enemy cities....without any means of defense (bomb shelters help if you can get to them fast enough, but only weaken the effect).
In simple terms, Nukes are a military unit without equal. Just like in any game, I expect that if something gives me the most power, than it has to have the most cost. Else.....why would I use anything else?
Now if I was building a game from scratch, ideally Nukes would be your final military unit. They are the capstone of all military power, and that would make sense gameplay wise. But due to Civs partial modeling of real life, we can't do that. Nukes come earlier because....that's how it works in RL.
Since we don't have the moral complexities of real life, than we need to use other mechanics to balance it. Either we continue to make it even more expensive than it is now, or find some secondary cost that deters people from just using them at will.
So all of this ties back into your point/question. Should nukes have a greater diplomatic penalty than a raze? In real life...debatable. In game terms, no question. Nukes are far stronger than a raze, and much harder to defend against. So if we said diplomatic penalties were "the way to balance nukes"....than they clearly should be harsher than a raze.
Now I'm going to circle back to my original idea. If we all think that diplomatic penalties are a good way to balance....than I think decolonization is a way to really drive that home. This isn't a nebulous penalty that may or may not affect your neighbors. After all, everyone in the world may already hate you. But taking away CS, that takes away power. It can immediately be seen as a diplomatic backlash against your actions. Whether its enough is still debatable, but I think its an existing game mechanic that really helps to drive the "diplomatic penalty" home in a clear way to the player.
You could take it as steep as you want. Remove any spheres the player has. If they are host, a new election is immediately triggered. They suffer a -5 penalty to votes in the WC for X years (or permanently). But I think if you are really going to put a cost, it should use strong game mechanics. The "diplomatic penalty" is just too weak to do the job.