Factual error: The Doctor sets the atmosphere on fire, but only the upper part burns. The atmosphere extends from the Earth's surface (where it is densest) upwards, and so the flames would come right down to the ground, burning everyone to death. Of course that wouldn't work with the plot, so artistic licence has been applied.
Factual error: Colonel Mace says the Sontaran ship is orbiting 5,000 miles (8,050 km) above the Earth. However, in shots of and from the ship in both this episode and "The Sontaran Stratagem", the Earth appears far too small for the ship to be that close, with the ship's true distance appearing to be well over double that. (00:08:34)
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.