[Rupert]

On top of that, an antimatter explosion from containment failure (like a beam weapon punching through it), will not be a nice neat 'Bang!' as all the antimatter reacts with matter at once. It will be a much more drawn out affair as the AM contacts matter, some it it reacts and shoves the rest away from the contact, and so on. The same amount of energy will be released, but over a longer timeframe, so the burst will not be so intense.

Also, killing the warhead is not the only way of stopping a missile. A hit that fries it's electronics will do just as well.