the show continuously goes out of its way to explain to you, dear watcher, why even his atrocities were ultimately for the good of all mankind

I also currently watch Fringe (middle of season 2). Up until this point I don't see it done this way. Maybe that changes later on. What I have seen is, that Bishop tries to justify his actions that way, though trying to graple with the attrocities, that he caused. Others - like Olivia, the main character - think of this with disgust. Yes, she steps up and uses, what was dealt to her by Bishop and Bell. But it is also made clear, that the attrocities are not justified and that the problem at hand with the two universes is conpletely and utterly Bishops fault. It many episodes the case involves Bishops and Bells own research, which did and does horrible things to humans. At the time of the show Bishop is different than before, but not completely. We constantly see the mad scientist without any qualms fighting to get the better of him.