There are a few ways to entirely disable nukes. Removing the units is the most obvious, but this takes some work as they have entries in other tables. The much simpler way is to make the Manhattan Project unavailable; set its cost to -1, move it to Future Tech, etc. Since the units require the project to be completed before they unlock, they'll never appear. If you really wanted to disable nukes, you could just make the project they depend on be the Utopia Project (cultural win) instead of Manhattan Project. Since there'd be no way to unlock them without winning the game, the problem goes away.
Now, removing nukes has quite a few balance problems. Without them, what do you use Uranium for? The only other uranium-using thing is the Nuclear Plant, so now you'd have even more cities with huge production boosts. And without them, what's to stop you from just conquering everyone?
A better solution, in my not-so-humble opinion, is to make nukes a bit less damaging. You can reduce the blast radius, or reduce the effects. Or you can do what I did in my own mod, and add an SDI project that intercepts nukes part of the time.