What a riot...
We are trained, in a hijacking (or similar) situation, to depressurize the cabin of the aircraft to do the same thing as a sleeping gas would. In doing this, it reduces the bloodflow to the brain, which will effectively knock out the pax and allow us to land the plane with minumum hassle. The oxygen mask system is manually overridden, and only the pilots and possibly the flight attendants would be protected against it through the use of oxygen. However, this process could take in excess of 20-25 minutes to have an effect on the passengers, and if by chance during this period a terrorist walks into the cockpit and see the pilots with oxygen masks on, well, if one of the guys doesn't have a quick imagination, then there could be trouble.
This would not kill the passengers, it would simply put them in a "hibernation" mode until normal air pressure can be restored. The downside is that by doing this, you run the risk of having to evacuate a planeload of unconscious passengers in the event of an emergency, which definitely could get hairy.