Just as an idea, the shift in tone might be less jarring if the Lin, Savior of Elfkind storyline were locked behind the current Maria sucker punch storyline. It's not perfect, but it does provide a "well, yeah, they *would* try to do something after that". Though I don't know if would interfere with other things you have planned... On the plus side, it shouldn't break save compatibility.
I have been told that most people don't seem to find it quite as abrupt a shift as I did, however, so... YMMV.