There is always an arms race. Better swords lead to better shields lead to better swords...Planetbusters need not destroy the world, if there were a mechanism for reducing their effects. A city dome, or ionized shield maybe, would reduce them to regular nukes rather than ocean makers. And future techs would make workers able to terraform ocean back into usefull land anyway. Or maybe you could have a tech that gives you a totally undetectable saboteur, so that if a city has this saboteur and shoots a planetbuster, it blows up on the launch pad. But the saboteurs are very high maintenance units (variable maintenance cost, yeah). Or maybe planetbusters could have totally unpredictable effects, which are randomly determined, so that you don't know in any game if they will improve the terrain (turn all the land to solid gold) or mutate the victims, turning them into supermen who will be able to defeat you, or work as predicted. Also, you could have planet buster resistant units, like modern armor that has a good chance of surviving a nuclear blast if it isn't too close, only this would be force field protected units.
(To mod planetbusters, just have a tech that makes cheaper nukes available and another tech that allows the production of no maintenance robot workers to clean up after them, and multiple antimissile wonders [would they stack?].)
Planet busters are inevitable, if you want to convincinigly represent the future, but need not be a game imbalancer, as counterbalances can easily be justified.