The stock boosts are clarified as having been secretly routed to charities for firefighters, cops, and registered heroes, so morally Tony comes out pretty clean there. The conspiracy to raise Atlantean tensions is obviously greasy along with many of the other things he did to drive the agenda, but he knows it was bad yet did it because he believed it was necessary. And Sally and Ben don't disagree. There were tangible gains to be made by having things like Prison 42 and pushing registration hard to bring the new status quo quicker, but they required immense personal and ethical sacrifice from Tony. The end of his arc for the event is the realization that it still wasn't worth it, and the Front Line's background details just add more meat to that. But it's always going to be an event where obviously questionable events are misinterpreted because of what the actual game being played was, and that's the main book's fault for leaving these things to be properly fleshed out by Bendis and Jenkins.
Those poems at the end of most of the issues, though. Those can go.