As someone who likes to keep their games tidy, I personally share your frustration with the Once Upon a Time packaging. It's my hope that in future printings, we will include a tray that keeps things neat.
I want to make sure I understand your question, though — what prevents you from rubber-banding the cards in decks before you put them back in the box? That's how I store my own, so I wonder if I'm missing something.
Thanks for being our customer, and I'm sorry that our packaging isn't meeting your needs.