I'm sure the secret identity will be back eventually, though I'm not sure how long it will be before it does come back, but I wouldn't be surprised if in planning for "Truth" the writers had a plan and made sure to leave an out for them to restore it once the story has ran its course or they've achieved their intentions with it.
I really don't see how we'll end up with a One More Day situation. Superman would never make a deal with the devil, he doesn't have a marriage to sell anymore or that DC wants to get rid of, and I highly doubt DC would do that to end the Wonder Woman relationship.
For all the criticism aimed at DC for their treatment of Superman, even I can't think they'd ever go so far as to do another semi-reboot on Superman and basically rip apart his core character and leave him a mess like Marvel did with Spider-Man
.