I don't know anything about Guts, so I can't really give a definitive answer, but it's doubtful that Frank would necessarily "do better" than Bruce. I think the Punisher could do an adequate job, but I don't see how Punisher's use of lethal force would improve his chances in Gotham. Batman, as an entity, is designed to tackle the specific threats that Gotham crime presents. His decision to not kill has rarely hampered his success rate, and Batman's effectiveness really comes down to Bruce's intelligence, diverse skill-set, and the ridiculous amount of resources and allies that he possesses.
The Punisher would probably have some success with low-level crooks like Kite-Man and Firefly, or non-powered crime bosses like Penguin and Black Mask. The crime rate would definitely drop if he used lethal force on petty villains and thugs. But the Punisher's brute-force method of crimefighting isn't going to work on all of Batman's rogues' gallery. What happens when Punisher goes up against villains like Joker, Riddler, or Bane; villains who have plans within plans, who think three steps ahead with contingencies, who will complicate Punisher's shoot-to-kill methods with dirty-tricks like civilian hostages or elaborate bomb threats? How will he fare going up against villains who don't share an established relationship with him, like they do with Batman? Villains who will have no problem killing Frank with the most extreme of methods, without giving him a fighting chance to stop them? That's not to say Punisher can't be tactical and intelligent (e.g. Remender's Dark Reign stuff), but not a lot of heroes possess the sheer cunning to go up against a mastermind like Joker besides the Dark Knight.
Or what if Punisher were to deal with Batman's more powerful villains? Ra's al Ghul and his League of Assassins, or the Court of Owls and their Talons. What good is lethal force against enemies who can simply resurrect themselves over and over again, who have had centuries to plan their moves? With armies of loyal followers and billions of assets to support their cause? Another point to note is that Punisher simply lacks the sheer volume of resources that Bruce possesses. He doesn't have a million-dollar company, cutting-edge equipment, established relationships with the city's political and corporate leaders, the police force, the media, the underprivileged; or an intelligence network, or years of experience growing up in Gotham etc. Frank himself rarely works with allies besides one or two people (e.g. Soap in Ennis' Knights run, or Micro, or the lady from Rucka's run etc.), and a war on crime against a whole city on Batman's scale requires an insane amount of manpower/resources. For all his reputation as a loner, much of Batman's success comes from his ability to recruit and inspire people. Or as Morrison puts it: "That's the first truth of Batman. The saving grace. I was never alone."
Also, don't forget the fallout from the Punisher using lethal force. Besides having the full brunt of the GCPD coming down on him, Punisher will also have to contend with Batman's network of allies. Just because Batman is off-planet fighting a god with the League doesn't mean that he'll leave his city unprotected. I don't imagine that a killer vigilante in Gotham is going to sit well with the likes of Nightwing, the Batgirls, Red Robin, the cast of Detective Comics, Signal, Bluebird, the other thousand members of the Batman family. So not only will Frank have to contend with his one-man war on crime, but he also has to deal with the full force of the law and a couple dozen vigilantes trained by the goddamn Batman. The Punisher is usually sequestered in his own corner of the Marvel U, dealing with the scum of humanity. But he generally doesn't operate on the scale that Batman does.
Now, maybe Guts makes it easier, I'd be interested to hear an argument for that. But "he kills!" is hardly the solve-everything solution to Gotham crime that it might sound like. Also, as Batman comics like Morrison and Snyder's runs have suggested, the city often adapts to its heroes by providing them with new challenges. Look at Dick Grayson in The Black Mirror, or future Damian in Batman in Bethlehem. What sort of monsters would Gotham create in response to a killer like the Punisher? Food for thought.
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