First, to cover 2 miles in 6 seconds with smooth acceleration you'd need to accelerate at somewhere around 600ft/s^2.
This would give a final velocity of 3600ft/s, or about 2400mph (sorry for all the freedom units, the article started it...)
Just double-checking, that means the distance covered would be about 3600ft/s * 6 seconds / 2 = 10,800 ft, close enough to 2 miles.
Fall damage should be related to kinetic energy I think, so if 60 feet is 2d6, we need to figure out how fast something is going after falling 60ft. That's about 60ft/s -- 60ft ~= 32ft/s^2 * 2 seconds / 2, 32ft/s^2 * 2 seconds ~= 60 ft/s
So the final velocity is ~60x for the rail gun, and the kinetic energy is therefore 60^2 = 3,600x
Therefore the rail would do 3,600x the damage = 2 * 3,600 = 7,200d6 damage. That averages to 3.5 * 7,200 = 25,200 damage, enough to kill just about anything?