Can Twilight heal while she is hidden within Magic? Or is she fully in suspended animation? Because if Twilight's still half dead when you find her in Canterlot, it's going to make your life rather excessively exciting.
Then again, as long as the anti-magic bubble is up, her usefulness in there will be severely constrained no matter her state. We'll just need her conscious in case we require access to her encyclopedic knowledge.