I don't believe that there aren't accurate, nonlethal, instantly incapacitating weapons (or the technology to manufacture them) that can be used on board an aircraft without endangering the aircraft. Surely such weapons should pretty much satisfy every concern I've read above or heard about on the news today?
Genghis: Ok, then give us a pointer to these wonder weapons. I'd sure love to see them.
Let's consider the non-lethal weapons that do exist.
Tasers certainly don't match the requirement. There are two types of Tasers. The first is a contact model that you have to hold up against the person. That's hard to do when the assailant is resisting. Even in the best possible case, they take 10-15 seconds to disable someone.
The second type of Taser throws two projectiles through the air, with wire leads attached to them. You only have one shot, and if you miss, then it doesn't work. If the assailant pulls the projectile barbs off his chest, it doesn't work. And even if the barbs stay in, they have failed to subdue more than a few EDPs.
As for defensive aerosol sprays, the main one used these days is OC (oleoresin capsicum) spray. Any US police officer will tell you that sometimes they work. And sometimes they don't. A committed assailant can fight through the spray.
There are three main varieties of OC spray: 1) stream, 2) fog, and 3) foam. Both fog and stream will result in the OC being recirculated throughout the cabin -- sure hope the pilots don their masks beforehand. Foam won't be recirculated throughout the cabin but it can be defeated relatively easily with sunglasses and be thrown back at the officer.
Some US police forces use bean-bag projectiles that are shot from pump-action shotguns. It would be rather difficult for a sky marshal to conceal a pump-action shotgun and a pump-action shotgun is a tad unwieldy for CQB in an aircraft. This could also probably be defeated in several ways using improvised soft body armor and/or creative use of a seat cushion.
There are various types of batons that can be used. For this purpose, the likeliest candidate is a collapsible baton like the ASP. It is a contact weapon, meaning that the officer must come into arms reach of the assailant (something that is always risky). It certainly isn't instantly disabling. Batons can be deadly if used inappropriately. And the likelihood of success is a function of both the officer's skill and the assailant's skill at CQB.
Sorry, but putting phasers on stun only works in Star Trek.