Cross-posted to my outdoors blog.
The FAA gives a report of 11 known stowaway incidents from 1947-1993.
Of these 11, 6 died. 2 of them had definitely frozen to death. 3 more fell after the plane made it to cruising altitude, and could have frozen to death. Another fell on takeoff. This means that you have a 55% chance of dying if you attempt this, and if you die the chance is 33-87% that you will freeze to death.
Of course it's likely that other fatalities occurred but were not discovered because the plane was over water or the body landed in an unpopulated area; it is also likely that people stowed away and were not discovered, so it's hard to say which way the sample is biased.
The mechanism cited as probable pathway to fatal hypothermia at altitude seems very likely to be the same one that explains the strange behavior of high altitude mountain climbers who succumb to a similar fate, and are found having taken off most or all of their layers. Under conditions of low ambient O2, the hypothalamus becomes hypoxic and can longer thermoregulate. In climbers, their frontal lobes are hypoperfused, and they feel hot and can't reason themselves out of/inhibit themselves from taking their clothes off in the middle of a glaciated mountain. Stowaways are crammed in and can't move anyway.
Management: don't be in a plane at cruising altitude outside a warmed and pressurized cabin.