That has nothing to do with the rocket launching from Earth (A rocket in space follows the same rules), and everything to do with the fact that rockets expend most of their energy to push their own fuel.
That fact is incredibly relevant for getting to orbit - however, it is not at all relevant for surviving re-entry, where all that matters is your kinetic energy.
The Earth part was just shorthand for the fact that the atmosphere and gravity of Earth add about 1.3–1.8 km/s of delta v to achieving the pure kinetic delta v of 7.8 km/s needed to achieve LEO [1]. The first stage adds almost all of this "extra" delta v.
I was mostly just correcting your "one-sixteenth of the energy required for orbit" statement. I agree that reentering at 7.8 km/s is much more difficult than 2.0 km/s, but the second stage is smaller and more spherical than the first stage. That might make reentering it a bit easier than if it had the shape of the first stage.
That fact is incredibly relevant for getting to orbit - however, it is not at all relevant for surviving re-entry, where all that matters is your kinetic energy.