What you are suggesting creates security problems for legitimate pilots in the flight deck. We will just have to accept the small risk of "Rogue Pilots" in order to protect the integrity of the flight deck.
It does if you look at the SLF as prospective terrorists. It might be wiser to look at them as the last line of security. Keep in mind that it wasn't the TSA gropers that stopped the shoe bomber - or the underwear bomber - it was the passengers. It was also the passengers who kept the 4th 9/11 plane from reaching its target.
Things changed on 9/11. Before that, hijacking pretty much meant sit down, shut up and go for a joyride to some third world country. Now, even the SLF realizes the rules have changed, and they are ultimately responsible for their own survival - and that of the people who know how to fly the plane. Pilots need to remember that the passengers aren't the enemy.