Far worse to kill in cold blood, and in the MU, that's not really an easy question--villains become heroes and back again a lot. It's more fluid and ambiguous, unlike the DCU where "good vs. evil" is more like a cosmology. So Cap working with them under these circumstances is not wrong, though he didn't look too keen on the idea anyway.
Also--Goldbug and the Plunderer? I can't imagine either of them did anything deserving that. Except maybe their choice of outfits.
The Punisher is not a hero, though he may do things that serve the cause of good. He's Batman if the heart had been taken right out of him, but with Vietnam experience and military training. Or Rorschach had he been a Marine once. Ennis got the character right because he wrote him as a man who knows his soul is dead. He also didn't treat him as a "hero." Nor "likeable", more like "interesting". And somewhat grotesque. He's that guy who stands at that point all "superheroes" try to stop short of. The best Punisher stories are ones that are chilling, rather than thrilling. At best, it seems to me, he should never seem cathartic, and should inspire, at best, mixed feelings. Otherwise he is a rather malignant character.