The problem is still detecting them, and getting enough of the anti drone systems into place. Also CIWS systems tend to be big, complex and expensive, what's needed for drones is something that can be made relatively cheaply in large numbers and be deployed easily as your front lines move.
A normal AA missile can cover an area that can be tens of miles with relative ease, and a relatively small number of radar stations is enough to allow for warning and targeting, with drones being so much smaller you'd need far more detection systems, and then if you're using something like a phalanx you're going to need a massive number of them as they're line of sight, relatively short range and you'd probably need to program in a lot of "dead zones" to prevent your anti drone system causing more damage than the drones it's trying to take down as you're likely to be firing at much lower levels and those rounds have to go somewhere (an AA missile or flak gun firing into the air tends to have the remnants of it's ammo falling to the ground, not being fired in such a way that misses are still moving largely horizontally at lethal velocities).
Counter drones is probably the best long term solution, even armed counter drones that can work alongside some form of cheap to deploy detection system, so the defending drones can then take off and act as a mobile attacking system. Something along the lines of a cheap drone armed with a small AA rocket that can pop up along the route of the attacking drone, fire at it and then either drop down for reuse, or if the distance weapon fails, try and kamikaze the incoming drone so you're doing away with the need for a ground based system with LOS (potentially you could design them so they can be deployed on the back of a trailer that any vehicle with a towbar can move, so everywhere you have a unit of troops you cna have a drone counterbattery, or you could drop off dozens/hundreds of drone stations where they are needed and redploy them quickly)..
