Well after the Proto Merkabah was seperated to stop it from destroying the planet of second miltia, part of it hit the side of the Elsa, damaging it's re-entry controls. So when the Else hit the atmosphere, they realised they were all going to burn up and die. Then the rear exit hatch opened and Kos Mos left the ship, planning to shield the Elsa with her energy shield. So yeah, thats why she's burning up. Her eyes are going blue in this shot, because she's about to grow massive white angel wings which shield the ship and allow it to survive the re-entry.