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First, she really is off the show for a while. Katee Sackhoff (Starbuck) did a radio interview the other day where she mentioned that she is definitely off the show for now. She's still locked in under contract, but they have released her to do other projects. She just filmed the pilot for a new show on NBC, and she's working on a movie for Lifetime right now. Whatever Starbuck's ultimate fate may be, we apparently won't be seeing it for a while.
Second, the BSG writers have borrowed story concepts from the original BSG before, often rewriting them so heavily that they only vaguely resemble the original. Fans of the original story may remember the Ship of Lights, a ship controlled by godlike beings that had power over life and death, matter, and even time (there was a suggestion that they may have been the distant ancestors of the colonists). In the original BSG, it was the gods in the Ship of Lights that eventually provided the fleet with the coordinates to reach Earth.
People on other boards have brought up the possibility that BSG may be planning on re-using this concept. If you watch the story again, you'll see quite clearly that the person she was talking to wasn't a Cylon, AND that she was bathed in LIGHT as her ship hit the atmospheric hard deck.
I would suspect that she's being written out of the story for a while. If I had to guess, we'll be seeing a returned "pure and godlike" Kara Thrace returning at some point in the far future to save the fleet from destruction, or to lead them to their destination. I would imagine that her return will not happen until they're ready to complete the story arc.
Of course, maybe she's just a cylon. It's also been pointed out elsewhere that her mother was a soldier in the first Cylon War who was decorated for combat. It's possible that Kara herself is a human/Cylon hybrid, and that's why the Cylons are so interested in breeding her. If her mother was aware that Kara was the result of a cylon rape, it might explain her anger at Kara for being so "normal".
Then again, maybe she's just dead. BSG wouldn't be the first show to re-energize a storyline by killing off one of its main cast members.
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