> The missile-defense system work by using SAMs (Surface-to-Air Missiles
SAMs aren't an alternative to nukes because SAMs can be nukes. The (retired) US Nike-Hercules (intended for anti-bomber) and Nike-Zeus (anti-warhead and, at least in testing, also anti-satellite for Zeus B) are examples.
(Note, if you live in the Bay Area there are a whole bunch of decommissioned bases for these missiles around.)
> Having a nuke counter an ICBM will lead to far worse fallout.
Nuclear airbursts that aren't in close proximity to the ground relative to yield have essentially zero fallout (fallout is basically irradiated debris from the ground kicked into the air by the explosion.) It may or may not increase the amount of flash radiation, but that's a shorter-term, smaller area problem. But the US doesn't (at least officially, and I doubt this could be effectively concealed) rely on nuclear air-to-surface defenses any more.
But any nuclear attack has an EMP risk, and I don't think a plane is where you want to be during an EMP. Plus, people on the ground when a threat is confirmed have a better chance of being able to follow an order to shelter than those in the air.
From a civil defense perspective, “ground the planes in the potential target area immediately and unconditionally on launch warning” makes a whole lot of sense.