Yet Captain America was perfectly willing to work with Punisher in Civil War, until he made the mistake of mowing down criminals in his presence. Because I guess simply knowing that Castle had a few hundred confirmed fatalities and had even gone to jail and escaped a few times for them wasn't the same as actually witnessing it. But I guess that falls under "Millar's a hack" too.
Has the Punisher ever killed someone who was "innocent"? I know Wolverine has done some very nasty things before Weapon X, even before ORIGINS started heaping more piles of *****e-bag stuff into his folder. Frankly it always struck me as weird that you never see anyone trying to go after Wolverine who has a legitimate grievance with him, or at least it is rare. Wolverine killed quite a few heroes in ENEMY OF THE STATE. The Slingers could all reunite to hunt Logan down and force him to at least stand trial for decapitating their buddy Hornet, and what would the New Avengers do? It's too good a story for anyone to actually do, though. And to be fair, SHIELD probably covered up the fact that it was Wolverine (in LONERS, Gallo seemed to imply that he didn't know who had killed Hornet, even if the art showed the reader).
Wolverine, despite all his barking about being a loner, has often teamed up with virtually every superhero on the planet for the greater good if it comes to it. There may be that unpleasant acceptance that when Wolverine is stable or on a leash, he is handy. Of course, you could say the same of Dr. Octopus. The morals are rather murky. They've certainly changed over the 21st century. In the past, the X-Men usually didn't encourage Wolverine to kill people, although they not as "anti-kill" as the Avengers used to be. Logan to be fair usually did his killin' during solo adventures, so the X-Men could claim plausible deniability. "I have no idea what Wolverine does at bars in Madipoor at 3 a.m., sir. I was busy crying over Maddie Pryor." Other superheroes used to frown at Wolverine about the same as they frowned at Punisher. Then in the post 2000 era, things changed. The comics code was zapped. Comics started trying to compete more with TV shows, movies, and video games. It quickly became okay to slaughter minions. Superheroes who used to simply TKO the nameless grunts of their enemies would sometimes either kill them outright (Iron Fist, Luke Cage) or not say a word when their allies did (Spidey in New Avengers is the easiest example). Hell, I remember one MTU issue where Punisher saves Spider-Man, Moon Knight and a few other heroes from Ringmaster by shooting his finger off and Spidey literally CHEERS him. For what? Not capping the villain in the head? And that was Robert Kirkman.
I think what has happened, besides the assumption that kids under 13 no longer read comics and thus the default "rating" is PG-13 at least on violence, was that some staples of heroics got altered with the new EIC reign and whatnot. People misunderstand some heroes being willing to kill in wartime situations like Cap or the Invaders as being the default, when it doesn't have to be. It's not an equal situation. A clan of HYDRA grunts is not the same as D-Day. But even on TV, rules regarding violence have changed for cartoons even.
Punisher is usually less willing to work with superheroes and he usually resents them. He has, though, albeit usually with Daredevil or Spider-Man. I wouldn't call them "the worst that humanity has to offer" before villains, though. Wanting to kill bad guys sometimes isn't a bad thing; everyone loves DEXTER, after all. In one of the CIVIL WAR specials, written from IRON MAN's POV, he noted his dislike at Punisher because the idea was that killing criminals didn't ever give them the chance to change, and he cited many heroes who started out as criminals (albeit they never killed anyone or really did much beyond steal things really). Of course this is the guy who recommended Wolverine for his team for exactly that reason, so hypocrisy all around.
It is a tricky wicket.