Trivia: The Shakri has only 8 lines in the whole episode.
Trivia: The events of the previous episode, "A Town Called Mercy", actually take place during the events of this episode, specifically at the end of the seven-week anniversary trip the Doctor takes Amy and Rory on. The evidence? In "A Town Called Mercy", the Doctor mentions Rory having left his cell phone charger in King Henry VIII's ensuite. During the montage showing the anniversary trip in this episode, the Doctor, Amy and Rory are shown hiding under a bed in the past, and a whispered conversation reveals they are hiding because Amy just accidentally married King Henry VIII.
Chosen answer: 1) When Stephen Moffat took over he ignored a lot of what had been developed before (there is not in-universe answer). 2) It would have killed Rose, so the Doctor absorbed the energy. His body regenerated before the energy could do a significant amount of damage that would prevent regeneration.