The Punisher has committed his life to a one-man war on crime, so why hasn't he already taken down Kingpin, Marvel's crime lord supreme? Frank has taken several shots at Wilson Fisk, but rarely with the same zeal as he attacks other major criminals. While the Punisher will happily take a shot at Kingpin if the opportunity arises, he doesn't go to the same insane extremes to take him down as with other criminals, but it's not because he believes Fisk deserves to live, as proved in countless alternate timelines.
Frank takes great pleasure in killing off a zombie Wilson Fisk in Marvel Universe vs. The Punisher, even taking his head as a prize. Meanwhile, in the Army of Darkness vs. Marvel Zombies, Evil Dead’s Ash Williams escapes death to end up in an alternate Marvel Universe just about the time a zombie Sentry begins transforming superheroes into ravenous zombies. In Army of Darkness vs Marvel Zombies #2 by John Layman, Fabiano Neves, Fernando Blanco and Sean Phillips, Ash is roped into accompanying Frank Castle through a building where locked doors are blown to reveal Kingpin alongside fellow crime bosses Hammerhead and the Owl. Although the Kingpin tries to negotiate with Frank, his opinion that the current apocalypse has changed the rules to humans vs. zombies means little to someone who never saw him as human. The Punisher executes all the potentially helpful allies without hesitation before a shocked and confused Ash.
Similarly, in Secret Wars #1 from Jonathan Hickman and Esad Ribic, two versions of the Marvel Universe are set to collide with each other, ultimately destroying both. Kingpin sends out an invite to other villains to celebrate, and it's revealed that Frank managed to intercept the message, showing up to end Kingpin and his flunkies before the world is destroyed. Punisher even makes time to target Kingpin in Punisher Kills the Marvel Universe - from Garth Ennis and Doug Braithwaite - even though his mission in this story is to wipe out all superhuman life. Perhaps the most devastating showdown between the two happened in Jason Aaron and Steve Dillon's run of Punisher MAX, where a grizzled version of the Punisher takes on Kingpin (including his assassins Bullseye and Elektra), ultimately dying to take down the crimelord.
It's this last attempt that shows why Punisher doesn't commit to killing Fisk until confronted by an apocalypse - he knows that in the normal run of things, Kingpin commands so many resources and soldiers that he will likely die in the attempt, leaving so many others unpunished. Punisher #18 - from Mike Baron and Whilce Portacio - also confirms that Frank knows removing Kingpin under normal circumstances would result in a war to claim his position, putting many innocent lives at risk. Of course, if the world is ending anyway, these issues quickly go away.
That's why when presented with an apocalypse, Frank Castle does everything he can to kill the Kingpin, no longer caring about the consequences or his own survival. Punisher knows that truly committing to killing the Kingpin has to be his last hoorah - the great hunt he's almost certain not to walk away from - but as a result, he also views any given apocalypse as a great excuse to finally end Wilson Fisk for good. This creates an epic situation where once the world is truly doomed, Punisher is finally free to set his sights on Kingpin, proving that he's got no intention of allowing Wilson Fisk to escape - he's just saving him for last.