How to make Kingdra a sad... Er... Seahorse?
Just stop its trainers. Game over. Who cares about Claydol, if they're never going to rare candy to Kingdra swarm you?
I don't honestly see many other "counters" honestly working against Kingdra. Raichu might be nasty once, and then Uxies come back and you've just night maintenenced and re-played the claydols. Whoops. Tangrowth SF almost works, if it could stop your bench from being slaughtered (considering how easy I found playing against Tangrowth tech yesterday, its not a real threat to Kingdra). Luxray's just... Bleh (10 HP too short on the thing :/).
...Seriously though, I wouldn't worry about Kingdra. Go freak out over the stormfront stuff that's even more rediculous :/