I would point out that any autonomous aircraft operating in an air traffic environment like the one we have currently will have to allow remote access to its FMS. This is the only way that route changes and other ATC constraints can be conveyed. Therefore many of the concerns regarding hacking into the system remain valid.
Precisely. If this isn't done, how will an aircraft be ordered to "go around" or enter a holding pattern? As I wrote before, what is technically achievable from an engineering stance is one thing, but fitting fully automated aircraft safely into the existing infrastructure is another kettle of fish altogether.