It's possible Kara could've gone into one of the nutrient cryo-sleep pods as the ship crashed. It'd basically serve the same function as an airbag, only it'd have to be deflated (read "deactivated") from the inside.
Plus, given that the pods seem to preserve the people inside, she'll retain her age. The question is why would the Jor-El AI (yes, I'm pro-Jor-El dying, sue me
) not reveal Kara's presence on the ship?
We obviously know that, since this ship IS the Fortress of Solitude that it left Krypton AT LEAST 5-7 years before it's destruction. Therefore Jor-El and Lara must have stayed behind after launching Kal-El into space.
Maybe Jor-El followed the Codex signature of Kara's explorer ship to the Sol system (by the way, how would the Kryptonians know that our system would be called the "Sol system"? Were they already aware of human life on Earth and simply adopted the name for the sake of convenience?) so that's how he knew to send Kal-El along that trajectory?