The most effective "anti-cruise missile" defense I've seen in-game yet, is, interestingly enough, the 57 mm AK-725 turrets on the Kresta II cruisers. They have the range, and the accuracy to nail ASMs at medium ranges. In real Life, that particular weapons' system was found lacking in that area, most likely due to poor interfacing bewteen the turret and its fire-control radar. It failed to stop an ASM that was accidentally fired against a Soviet Corvette, resulting in casualties.
The Kashtans are OK against cruise missiles at long range (when using its Kortik SAMs). At shorter ranges, however, the game engine somehow gets confused when choosing between missile and gun mode, causing the gun-barrels to stay elevated somewhat above the flight-path of most surface skimming missiles.
The AK-630 turrets don't have that issue.