Even the infidel Johns has become a true believer... I hope,cant wait to see this Batman display time travel and omniscience. But seriously, I dont see what the big issue is? most likely he'll have all knowledge in the universe for a brief period. Morrison did this already in Return of Bruce Wayne,Batman is still Batman today despite that and knowing Johns he'll use this opportunity to knock Batman down a peg.
I also dont recall anyone complaining when Doom and Thanos find magical hearts and gloves that allow them to enslave the universe,how exactly is this any different?