This is an interesting dilemma. But basically, it is unlikely the 4-5 people could kill everyone on an airliner without access to the cockpit. You could cut a couple of throats, but then the rest of the pax are likely to start fighting back eventually atleast slowing the terrorists progress if not stopping them completely. IN the meantime, you can hustle the aircraft onto the ground where you can get some armed intervention.
As soon as a terrorist gets into the cockpit, he only has to kill 2 people (the pilots) to kill the rest of the people on the aircraft. Handgrenades inside the cabin aren't sure to bring the aircraft down either, unless you throw a lot of them....
Certainly on a 747 the easiest way to kill 400 people is with the controls in the cockpit.
As to the needs of going back to the cabin. The freighters never have that option. the 757PF that UPS flies has the number one door moved way forward. Behind it is a solid bulkhead. In the cockpit area is a mini galley and a lav. Use that as the new standard and place the pax cabin behind the freight bulkhead with no cockpit to cabin access.
As to evac routes, the pilots still have their outside door plus 2 windows. Cockpit windows are never included in the certification for an evacuation so that doesn't change anything either.
Inspection of gear ports and what not can be done with video cameras.
Cheers
Wino