There are several already deployed defenses against these, and weapon systems similar to these. The basic chaff deployment systems, CIWS systems for close in defense, and several anit-missile missile systems can all be leveraged to provide defense against an incoming attack.

Additionally, the strongest carrier defense against weapons such as this is the size of the ocean, and their short(ish) range. You can't hit what you can't find, and/or what you can't get close too.