The Wedding of River Song - S6-E14
Other mistake: When the Doctor walks into the control room at the base, the time on the computer is frozen between 5:02:57pm and 5:02:58pm. The Doctor grabs River's hand, and time begins moving up to 5:03:00pm before he is restrained. Later, when the Doctor and River kiss and time begins moving again, the time is 5:02:00pm.
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.