One pilot takes out the other by any of a variety of quiet means.
Remaining rogue pilot wants at least to protect his name and his family so programmes the auto pilot on the path of twists n turns n subterfuge that ends as we know in the remote southern ocean ... this programming will take it to 45,000 ft for at least say 20 mins soon after the auto pilot is activated.
Rogue pilot takes out transponders and comms, begins to depressurise the plane and hits the pre programmed auto pilot ... 20 mins later all on board are dead and a ghost plane flies on the pre programmed route till fuel runs dry.
