More Security
The way pilots can defend an aircraft are limited in the air but can be very effective. The first, less destructive, and more deadly is lowering the cabin pressure. The second way is potentially dangerous and is only partially effective would be to maneuver the aircraft.
All modern airliner aircraft have a pressurization system. Commonly, the aircraft flies at over 25,000 ft (the only exceptions tend to be puddle jumpers [turbo props]). At these altitudes, time of useful conciousness at altitude without supplimental oxygen is measured in minutes and can go as low as seconds as aircraft go above 35,000 ft. The pressurization keeps the aircraft in the 6,000-8,000 ft range, which is comfortable for most people but is still noticeable.
The pilots have two ways to vent the atmosphere: raising the cabin altitude at a controlled rate or dumping the atmosphere. Either way, the pilots would be relatively unaffected because they are equipped with pressurized oxygen masks running off the engines or a seprate O2 bottle. Raising the cabin altitude would max out about 12,000-15,000 ft. At this level, most people are becoming euphoric, attention to detail decreases, and skill level decreases. This would slow the terrorists down. The problem is that people that are in better shape and who tend to live at higher altitudes are less affected, so there isn't a set reaction to this defense and it isn't 100% reliable. The second problem is that it will take a few minutes to begin to set in and isn't an immediate solution.
The dumping of atmosphere is a very drastic measure. It has the ability to cause perminate injury or kill passengers. Essentially, you go from 8,000ft to 25,000+ ft in a few seconds. The atmosphere in the aircraft can actually fog up and create zero visibility conditions (hindering any attackers and reducing the ability of the passengers ability to put on their masks). The temperature will drop drastically down well below freezing. Anyone with sinus or ear problems will have problems with fluids draining out of their sinus' and ear canals. Only those who are able to put the masks on very quickly when they drop will be concious in short order. Anyone with breathing problems will not survive long at these altitudes, and those even in the best of physical shape will follow them. The upper atmosphere is one of the harshest enviroments known to man and the pilots and passengers will be exposed to it in a very real way.
Maneuvering the aircraft is a non-lethal way of foiling a terrorist attack. The issue is that modern day airliners are not designed to pull multiple G or negative G maneuvers. Even a 0 G pushover can create problems with oil and fuel systems in the engines, not to mention the stress on the airframe. The idea is to stall the attackers while an outside force (either the passengers, the pressurization system, or another defensive mechanism) readies it's self to defend the pilots. In the end maneuvering is only partially effective, can only stall the attackers for a short while, and is dangerous to the aircraft. Such as it is, many pilots consider this an option due to the nature of the threat they are taught they might encounter (where surprise is key, and a delaying tactic of this type is a useful tool).