I was thinking about how much everybody and their mother having an MP has lead to really, really destructive wars and how it has kind of screwed things up. However, we obviously can't take MPs out of the game overnight and screw a bunch of people over, either. So, what I suggest is significantly raising the cost of nuke upkeep as the number of nukes you have on hand increases.
Currently, this is set at 10% more for each nuke:
In addition to the initial cost, nuclear weapons also have a starting cost of $5,000 a day to maintain (Upkeep cost is doubled if you do not have access to Uranium). This cost increases +10% for every nuclear weapon that you own.
So, for my nation right now with uranium and 19 nukes, my upkeep costs for nukes are a little over 200k daily. This makes it pretty easy to maintain full 25 nukes at all times on an economy of just 4k infra (what I had rebuilt to before I had to go fight Kaskus), but I have seen nations even lower than that running a budget surplus with full nukes.
If we were to up this number to, say, multiply the upkeep cost by 1000% for each new nuke (or something like that, I'm less arguing the number than the idea behind it), this would keep smaller nations with nuclear weapons from being able to just sit around with 20-25 nukes on hand at all times. In order to keep their economies running efficiently, they might only be able to keep 2 or 5 or 10 on hand at any time, else they might even risk running a negative budget until they start getting up into the WRC-level infra ranges where they can really afford. This also adds a bit more strategy to nation building, preparation for wars, and the wars themselves; and also helps to keep the majority of nuclear war in the upper tiers where nukes were originally intended to be. However, it also allows people to keep the wonder they invested so much money into and doesn't completely revamp the game mechanics. Additionally, because this increasing upkeep cost already exists in the game, it should be very simple to just modify the number.
On implementation: I'd give people like a month in advance that the change is going to occur to give them time to either use their nukes, lose their nukes, or accept having to pay more for nuke upkeep.