Flying by instruments, I wonder how high the risk truly is. One of the bigger concerns might be an instrument failure, like the failure of the airspeed sensors on Air France 447.
Very very high. What fuels a thunderstorm is large amounts of air rising, and falling very rapidly. When the aircraft encounters those air movements it can very quickly exceed the structural limits of the aircraft.
Some more detail: flying in rising or sinking air isn't a problem in itself, as long as you can tolerate the change in altitude. But flying from one into the other, fast, is a sure way to exceed structural load levels.
There were many failures in the cockpit of AF447. Almost all of them were aft of the instruments.
Problem exists between keyboard^H^H^H^H^H^H^H^H yoke and chair