The turn shortly before the transponders were powered down may have been the result of an FA's advice to the cockpit that men had descended into the E&E bay. The pilots, noting a loss of comms, may have decided that their only option was to turn back and await further developments. Navigation and flight control could've then become increasingly difficult as systems were rendered inert.
You really believe that in this post 9-11 world, 200+ passengers are going to calmly sit there and allow a couple hijacker/terrorists access to the area, especially when there's a FA standing there screaming "Stop them!"???