2-120kg is more than sufficient to fit an Rasperry or Arduino based autopilot. In fact, the computing power a drone can carry nowdays is perfectly fit for the purpose of targeting and homing in on the CIWS.
So jamming helps only against people taking the piss. It will not stop people taking a couple of kg of high explosive instead.
The real solution here is neither shooting, nor laser, nor jamming - they have the issue of range. Their range is too good so you cannot use them close to the shore and in-port.
The real solution, however is all around a ship all the time. It is called water. I have yet to see a 2-120kg drone which is capable of surviving a mining grade (not the wimpy ones used by the police) watercannon. Range is also perfectly appropriate - > 100 meters on specialized versions so a bow and aft mounts can cover even a ship the size of Queen Lizzy.
Anyone with a drone capable of surviving this, please come forward.
There is an existing cheap and shipping (with a sizeable install base) navalized version: http://piratesafe.com/