Clara in season 7B lost her dashing young gentleman time-travel partner and gained another, strange guy in his place. Series 8 Clara had a boyfriend, but then he died too. And she also realized that this time-travel stuff is kind of addictive and really, it's the life she wants. "Flatline" showed that she was good at pretending to be the Doctor, and that probably put some ideas in her head.
Series 9 Clara no longer has an "anchor" in Danny. She's still a teacher, sure, but for all intents and purposes she sees herself as the Doctor's partner. She wants this life. She wants to know "the rules." First the Doctor tried to tell her there was only room for one "him" in the TARDIS, because he was concerned about her trying to live the life of a timelord when in fact she's human. Get a hobby. Get a boyfriend. But...this is what she wants. Kinda like DoctorDonna, she wants to travel with him. An earthbound life isn't good enough for her anymore. She's gone "all in," and that's what the Doctor is partly concerned about. He can regenerate -- she can't. If something happens to her, or if she truly realizes that she can't do this forever....
But at the same time, he loves her and wants her around. He sees her as his partner in crime. "We're time travelers," he said a couple episodes ago. So I think her character arc is quite clear. She's given up her earthbound life and wants to travel in the TARDIS, whatever the consequences. And there will ultimately be consequences. I don't think this year's storylines were necessarily affected by Jenna's decision to stay at the last minute. It seems like a natural progression for her character.
Not what I personally would've picked, but if they're going for a gut-punch...