Nukes in CiV to the best of my knowledge is currently unstoppable.
Its gonna hit you full force in home
Pity there's no desertification in this civ. I like that aspect in civ4 XD
The desert fairy magic mechanic in civ IV was one of the stupidest features in any game:
1. Gameplay Balance check: FAILED. Reason: any source of global warming (actually desert fairy magic DFM) hit tiles on the world at random, without any bias toward people who caused it.
On average, it penalized all empires equally, never managing to change the relative position of civs in the game meaningfully.
2. Realism check: FAILED. Nukes couldn't possibly cause that particular effect in real life. Nukes wouldn't even cause DFM in the traditional sense. Also, the timeframe scale of fallout was off-kilter; if you had nukes early it was possible to have 100's of years fallout which is longer than any nuke's effect in history.
3. Player-controlled outcome: FAILED. In any reasonable game that made it to modern era, DFM happened consistently, regardless of nukes, every civ in the game running environmentalism (which actually opened the door to making DFM worse because health didn't benefit anti DFM while
increased the odds). Essentially, any reasonably high level game that made it late saw DFM without exception. What's the point of a mechanic that always happens and is always a penalty to everyone? All that does is create a universal nuisance. If you're going to do that, why stop there? Why not just play really loud noises and rotate the screen 90 degrees at random? Those make just as much sense.
Please don't support flawed, pathetic, ignorant design decisions whose sole purpose in the game is to annoy the player. It doesn't reflect well and it will hurt everyone if the designers get it in their head that it's a good idea.
As for nukes, right now there's no counter which SUCKS. IV did nukes pretty well; they were very strong with a tech lead or parity, but SDI made even tactical nukes reasonably cost-ineffective. Political hatred over them was higher too, which is reasonable for an uberweapon.
You are on the clock in civ V; get a big enough lead late-game where you can out-nuke everyone (or nuke pre-emptively) or avoid war entirely/get a scapegoat that's closer to absorb them. Until they add SDI that's all we've got.