I don't believe Joseph Kennedy was shot down:With the number of untimely Kennedy deaths (not to mention other events leaving to the term "Kennedy Curse") beginning with Joseph Jr shot down in WW II, in incidents ranging from skiing to drug overdose to assassination, I personally don't think invulnerability was a big issue on this one.
More like a particularly unhealthy case of get-thereitis coupled with distractions in the cockpit.
Kennedy and Willy remained aboard as the BQ-8 completed its first remote-controlled turn at 2,000 ft (610 m) near the North Sea coast. Kennedy and Willy removed the safety pin, arming the explosive package, and Kennedy radioed the agreed code Spade Flush, his last known words. Two minutes later (and well before the planned crew bailout, near RAF Manston), the Torpex explosive detonated prematurely and destroyed the Liberator, killing Kennedy and Willy instantly. From Wikipeadia
On another note, does anyone know if John Kennedy's aircraft was equipped with an autopilot?