Interesting question! But the idea of dropping a molecule won't get you the right answer. It's a standard problem in thermo courses to calculate the 'lapse rate' of the atmosphere, i.e. how rapidly temperature falls off with altitude. And the argument used there can easily be extended. The key assumption they make is that the temperature and pressure changes are adiabatic. I won't go through the steps but they wind up with
dT/dz = - (γ - 1)/γ (μg/R)
where γ is the ratio of specific heats cP/cV, μ is the molecular weight of the gas (grams per mole), g is the acceleration due to gravity, and R is the ideal gas constant. What's different about the problem you suggest is that g varies on the way down. In fact as you fall down the hole it diminishes linearly: g(r) = g r/RE, where RE is the Earth's radius. So using that, we can say that
dT = - (γ - 1)/γ (μg/R) (r/RE) dr
or integrating from r = 0 to RE: (just ∫r dr)
T = T0 - (γ - 1)/γ (μg/R) RE/2
What a mess! But everything in there is a known constant. g = 980 cm/sec2, R = 8.3 x 107 ergs/deg/mole, and RE = 6.4 x 108 cm. For air, γ = 1.4 and μ = 28 g/mole. Multiply out and you get (I think!) T - T0 ≈ 30,000 degrees K.