Oh, dear. Ever since it became evident that Nikki Reed couldn't act worth a damn, I've been afraid that the show would find some way to bring her out of the forced, contrived flashbacks and into the present. As soon as it was revealed that Betsy Ross had been in the Catacombs, I knew she'd probably be found alive there at some point. And now the day I've dreaded has come at last. I was hoping the producers would've realized by now that she was this season's Hawley and changed their plans in order to write her out. I guess there's still hope that she could make some heroic sacrifice in the season finale, but I doubt we'll be so lucky.
As for the other big tragedy, I couldn't bring myself to care. Joe never really interested me that much either, nor did his relationship with Jenny. And I guess I was distracted by the huge contrivance of Daddy Mills turning out to be yet another of Corben's unrevealed partners in monster-hunting.
I don't think the plot logic entirely tracks here. The Catacombs are supposed to be a place where time goes ten times faster than in the real world. Abbie was subjectively there for over ten months while only a month passed in reality. Ichabod and Abbie went in well ahead of time, with a plan to restore Pandora's Box before the Hidden One could run out his hourglass. And yet they hadn't even started yet when time ran out and TH1 got his ultimate godlike power.
Also, what good was Pandora's plan to disrupt the ley lines when TH1 was able to defeat it with, literally, a wave of his hand? It was pretty much just a way to give the characters something to do until the climax.