I'm going to take a page from Identity Crisis #6 and ask: Who gains?
Who gains from Arachnos no longer being in charge of the Rogue Isles? Who gains from Wyvern no longer existing? Who gains from _you_ no longer existing? Who gains from Dr. Miller dying? Who gains from the Breakout never happening? Who gains from the 5th Column existing in South America?
Looking back at the newspaper articles, something caught my eye: 11.1.3 says that Arachnos was behind the attempted Zig breakout, and that they were operating out of the Rogue Isles. It also shows that it's Ms. Liberty who sends in Longbow. But 11.2.4 says that Marchand repulsed Recluse back in '63 (and presumably pushing him out of the Isles), and it's now MRS. Liberty. Is it possible that whoever is altering time is making multiple trips, changing some small thing and then seeing how it affects the present?
Here's something nobody has mentioned: is it possible that it's the HEROES who have gone back in time and messed things up? Perhaps Statesman went back and tried to stop Arachnos from forming by helping Marchand fight off Recluse-which would explain why he's on good terms with Marchand in the latest City Scoop.