Now that I think about it a little more, automatic realitation doesn't really make much sense in a turned based environment. The main thing is to design it so the player that fires first doesn't have an advantage or at least a small one.
Yeah actually I've never been nuked in Civ 3 (in contrast to Civ 2 where it would happen *all* the time) or used nukes, so I'm not really sure how balanced it is right now. If I remember correctly, nukes have a 50% chance to take out each unit within 3x3 tiles, right? So conceivably you could take out 50% of a player's nukes on the first strike (except for tactical nukes on subs and away from the cities) if you targetted one missile for each city with a nuke, or 75% with two missiles, and so on...
Adjusting those values so ICBM's have a less chance of being destroyed in a nuclear strike might solve the problem. Maybe make it only 10% with an additional type of ICBM that has greater accuracy that would raise it back 50%, and have the number of those "first strike" missiles destablize things and make other civ's more likely to use their nukes, as they would be if you were building SDI.
I'm liking the idea of some sort of nuclear disarmament option, either a wonder (maybe instead of or in addition to SDI) or some sort of diplomatic agreement you could make with another civ not to build nukes. Actually things like that could bring a whole new diplomatic level to the game. You could have all sorts of military diplomatic agreements, like you agree to build no more than 10 battleships, or have this large an army, or whatever. Force a civ you just defeated to limit their army and any breach would give you a cassus belli.