With time literally on their side, Carter could have come up with multiple options: She could have sped up the time dilation slightly to allow the beam to hit the Ship at 1/1000 intensity. The ships hull would be able to handle that. She could have had more than enough time to repair the shields and perhaps even create additional shield generators. She could have literally disassembled the neck of the ship so that the ship would not have been hit by the Ori Beam.