Visible crew/equipment: When the Cyber-arm is shooting at the Doctor and Amy, there is a brief shot when the Doctor is talking where you can see the crew member who is shooting at them.
Visible crew/equipment: When Amy is guesstimating Amelia's age, the camera pans to the right and into a crew member's arm. (00:13:49)
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.