Thanks for pointing this out. It was probably the exact sentiment you described that influenced my judgement: the run came to a conclusion which seemed suiting. A page later (in the tpb) Frank is back with the Commandos and goes on a rampage which seemed to ignore the "real" end of the run.
I also get your point about the Superviallains but remembering the Frank from the Punisher War Journal Mid 2000 books (Civil War, Secret Invasion) I could picture his motives vividly. The event context really took over I guess but in my mind only half-baked.