we wrote our names on each other in permanent ink

That was not the plan for the Second Coming. That would have caused a war between heaven and hell that killed humanity and destroyed earth.

Michael wiped out humanity, earth and the entire universe by destroying the book of life.

No Alpha Centauri. Nowhere for them to go except staying in an empty bookshop with nothing else and God and Satan being able to pop in whenever they want?

God basically gave them a choice between having it all back as it was (with them never being free of heaven and hell and inevitably having another Second Coming, a Great Plan and war that destroys earth) or living in a world of nothing forever.

Instead they chose to break free and make a new universe were none of that could exist, including them and including God.

They would never have been left alone, heaven and hell always dragged them back into it. They would have never been free, or happy together. So they stood in front of God and told her to go fuck herself.