Kara Thrace is a woman of contradictions, born of a pianist (father) and a soldier (mother) Kara is most assuredly the product of such a strange union. She is at the same time the strongest and most vulnerable member of the rag tag fleet. All of her life Kara has been told by her mother that she is special and she's beaten the message into her literally. Thanks to this Kara has spent her life embracing and running from this idea. The moment she gets in a viper the first time she knows she's not just good, she's fraking great, but she's always making mistakes and lacks discipline (as she is constantly reminded). In the miniseries she's the hotshot pilot who misses out on the first battle because she's in the brig for punching a superior officer. A perfect summation of who she is in one aspect.
Things change for Kara when she is sent to interrogate a Cylon prisoner, a man named Leoben. When she meets him, Leoben knows her, he knows her mother, he knows her destiny (which she is reminded of by the oracle in this episode). And in a strange way he touches her. The moment at the end of the episode (Season One's Flesh and Bone) when she prays for him has always touched me deeply and I've always kept it as a true indicator of who Kara is at her heart.
In Maelstrom she's finally forced to confront all of the aspects of her history and what it is her destiny means.
To do this she must meet God and then confront the most painful memory in a life full of them. Kara learns that you have to let go before you can become.
As for dealing with the larger nature of the show, the story shows the deeper connection between the Cylons and the Humans that has been the main focus of the Third Season (and in many ways the show itself).
I have to also point out that if this was truly the end of the character's arc I would have been overly disappointed but as a turning point for her and the story in general it's beautiful and it's heartbreaking. And it's absolutely the right move.