I think that "all existence" is simply the batter's perception of his own reality. He thinks he's on a mission to purify the world. This "world" is really small. In my interpretation, each of the bosses of the zones are one of the Hugo's friends (based on the final area, "The Room"). Therefore, the emptiness that the batter leaves in these zones is possibly representative of the emptiness in the lives of those families. So he's not ending the world, just destroying peoples' lives.
As for how much the family screwed up. I don't think it was one thing. The Queen says something about a carnival, perhaps a birthday party for Hugo. There was probably a big argument, but we never get any details on what actually happened at this party. Also, Hugo was noted as being sickly. It's possible that the batter just didn't want to deal with it anymore. I'm pretty sure the batter does a murder/suicide thing, where he kills Hugo's friends, Hugo's mother, Hugo, then himself.
I'm not super sure about the comic book segment, apart from the fact that it is probably another clue that the batter isn't a good guy and his mission isn't pure (note that the enemies in this segment are baseball players). There are other clues, like going back to other zones after they were "purified" and finding REALLY weird music, whispers, distant screams, and weird baby/wrestler things. Everything is white, and soulless. Doesn't seem "pure," more empty and horrible. Another clue is in zone 3, when the batter and Zachary are on the tram, and it stops. An Elsen is there (who the batter promptly attacks), and he doesn't fight back (much like baby Hugo), and only yells "HELP!"
I'm unsure as to what or who the Elsen are supposed to be. They're all really skittish, ("Um... ah..."), and the ones in zone 2 are just afraid to do anything. I also haven't really though about the meaning of the specters themselves, but there's probably something.