The animation was created in POV-Ray 3.7, using as input data only the global true color mosaic projected onto a sphere. The atmosphere is modelled as scattering media with a strong directional component as is expected for haze due to particles.
However, it has to be noted that the light levels are fudged. Even though both LORRI data sets were acquired using the same exposure time (150ms), the released raw JPEGs are autostretched so the relative brightness is not (publicly) known. However, one constraint is that the atmosphere does not show up in the dayside images. Keeping the atmosphere model just tenuous enough for this, I had to boost light levels by a factor of 4 on the night side to reproduce the lookback image.
While it is likely the animation does not faithfully represent what you would actually see orbiting Pluto, we must also consider that our eyes adapt to ambient light levels. So if you can shield your eyes from the Sun while looking at the night side of Pluto, what you see might be what you get after all.
Some further fudging relates to the fact that mapping only a single image onto a sphere is not a good idea for 3d rendering and will cause ugly artefacts near the terminator. I cheated to cover this up; while we fly around Pluto the terrain creeps a little bit along with us (must be those glaciers).