@farmerman,
All the aircraft I flew and all I know of had/have redundant means of quickly disengaging the autopilot (or AFCS = automatic flight control system in jargon). We routinely disengaged it in any mode but clear air level flight.
Modern transport aircraft, necessarily constrained by the economics of fuel consumption, increasingly invoilve the far more extensive use of ever-more capable and programmable autopilots. For example it is relatively simple to use a computer input to program the optimum fuel consumption profile for whatever air traffic control constraints might be applied (i.e. best angle of attack, meaning you slow down as the aircraft burns fuel and gets lighter.)
The best and safest technique for penetrating an area of heavy turbulence is to slow down a bit from the best efficiency speed and fly at a constant angle of attack (i.e. pitch attitude), riding the currents up and down as you go. That generally involves manual operation of the flight controls.
Much speculation is afoot regarding the possibility of ice accumulation in the Pitot tube, which could have reduced the measured ram air pressure (=Vsquared/2g) relative to measured static pressure, yielding an erroneously reduced indicated airspeed. This is a primary flight instrument both for the pilot and the AFCS computers, however large transport aircraft have multiple pitit tubes & backups. There are other backup sources including angle of attack and GPS-derived groundspeed instrtuments, but, since indicated airspeed is much less than groundspeed at high altitude , and many civil pilots are unused to closely monitoring angle of attack, a number of subtle and insidious scenarios can easily be envisioned.