ICBMs travel in excess of Mach 10, and typical SAMs are Mach 1 to Mach 5.
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Instead of using a small explosive to bring down an enemy nuke, surely there's an idea to use a bigger counter-nuke? Sure, there's going to be a ton of fallout, but that's still better than losing the entirety of San Francisco.
Its a lot easier to hit an enemy missile with a big-bomb, rather than using a little bomb. IE: load those SAMs with nukes and have at it. Even if you're slower, you got the strength and blast-radius of a nuke and have a better chance of bringing down the enemy ICBM.
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I don't think its an issue of "airplanes would be hit by a SAM". I think it's seriously the risk of airplanes literally getting caught in the blasts (that were aimed at the enemy missile).