I noted this idea in Bruce Schneier's blog just after 9/11 back in 2001. I'm surprised that Boeing were able to patent it as it's so trivial to think of the idea. I'm certain I can't be the first person to come up with the idea as I'm just SLF and not in the aircraft flight computer business.
However, emergency auto-land makes perfect sense from the security point of view: deny the aircraft as a arbitrary destination flying bomb or as a traditional hijack situation (a la the 70's and 80's). It will not stop those who want to just blow up the aircraft who have figured out a way of doing that. Two out of the three major hijack modes completely dispensed with. History has shown that hijackers have never succeeded once back on the ground.
Arming pilots is a stupid idea - it just adds additional arms on a plane already equipped with many tonnes of fuel and an axe.
Solidifying the crew door is a good idea as it makes entry to unauthorized individuals much harder, particularly as PAX seem willing to fight back now, thus allowing pilots to land the plane quickly before the door can be compromised.
Physical security is not about absolutes, it's about deter, delay, and detain. Autoland is deter - there's simply no point any more. Hardened doors and better PAX screening is "delay". One day, someone will crack it especially as screeners are increasingly trained to be unbending and unthinking automatons.
This is a good addition to the threat model, even if it's not implemented widely. A sign saying "autoland fitted" is just as good as the system being actually installed as the attacker will not know for sure unless accompanied by inside knowledge.
Andrew