Well, the reply would have to be along the lines of the phalanx system - gatling-type shotgun with tungsten or depleted uranium projectiles. The thing to work on is the time to the maximum speed of the automatic fire burst - it ought to be decreased to a fraction of a second, together with the deneral agility of the system. Sounds like doable work.
Also, I presume, further work on keeping anything from getting too close to the carrier. That's what a carrier group is for. But it could be difficult in places like the Gulf.