You're giving them an awful lot of credit there in believing they realized there was nothing more to Zelena's story. Considering they brought her back the next season, I thinking that wasn't their thought process. It would have been just as easy to send Emma and Hook to Oz through the portal than to the Enchanted Forest past.
Mostly, I think they just get bored with their season arc and like to bring in a shiny new toy for the finale. It's where the "Wouldn't it be cool if...?" writing process takes flight because it's really easy to apply this in a two hour block and not have to put any thought into stretching it out over a whole season. It's also why the newly introduced storylines for the next season fizzle almost instantly. They aren't thinking about it long term when it's introduced and are bored with it by the time the new season starts.
This episode encapsulates every major problem the writing team had. There's little conclusion to tie up loose ends, there's no follow through on what should have been deeply emotional events in characters' lives, shiny new toys are introduced in a new world with nonsensical world building, repetition of events we've seen ad nauseum, characters act completely contrary to real world people simply because the plot dictates it, etc. All of it made for a really lack luster and frustrating finale.
And, because it must be said, especially for this episode, Shut up, Henry!