Will the first person they shoot at be a terrorist or a human shield whose body gets pushed towards the pilot as he emerges from the cockpit?
STC , the only people who assume the armed pilot will leave the flight deck in this discussion are those arguing against guns. The only purpose in arming pilots is to defend the flight deck, preventing the aircraft being turned into a missile. True, the odds are infinitesimal, but being struck by lightning twice in the space of five days (some times ago) dented my faith in those kind of odds!
cargo boy , your scenario (the flight deck being rushed at feeding time) is the biggest problem. However, some of the extra equipment being fitted to allow the flight deck crew to see who is at the door, and near it, should help prevent this. In addition, the proposed door locking system proposed by ATR (I think, the article in Flight International was some time ago) would make it impossible for anyone to override the flight deck door locks as long as either pilot wanted to stop them- without, however, stopping the cabin crew getting in in the event of crew incapacitation.