I agree this could be done, but this does not mean the copilot should not be pulling the heat. Whats the harm in having as many tools as possible?
Also I am certain the pilots in 9-11 did not have the 1 second you postulate. By the time the were aware of strangers in the cockpit, their assailents were on them. (I am not sure you can get that much inertia moving in one second either, but I am an aerospace engineer, not a comercial pilot, so I will defer to them). I will grant that with enough time and everyone but the terrorists strapped in, the pilot could make life misserable for them. While they are puking on the cabin floor, the co-pilot could put a bullet between each of their eyes, (If I were on the flight I would volunteer for clean up duty.) Cheers.
The pilots should never have been disarmed.