For his motivations, the Punisher isn't made out to be a mindless killer in the story. He goes through all the assassinations in a very methodical, Punisher sort of way (and I acknowledged that the nuke bit was a bit silly).
As for the threat from afar, I would say that overlooking the Brood, et al. was one of the things that was glossed over due to the enormity of what the title described. I used the Silver Surfer as an example because it would've taken considerable effort on his part to kill a man who can travel faster than the speed of light and is able to transmute matter at will. Even then, though, how would the Punisher have been able to take on Galactus? You could make the argument that killing a herald would give him powers, or some such nonsense, but the bottom line is that stuff like that doesn't belong in a Punisher storyline.
In short, saying that the Punisher is killing every superbeing in the Marvel universe was a bit overblown. It was really just an excuse to get the Punisher to take down some of the most recognizeable heroes and villains. I think Ennis did the best he could, given the topic.