This is a discussion topic for the Ore project, DisableSkeletonHorse. View the full project on Ore for downloads and more information.
Special thanks to http://pixelmonharmony.com for sponsoring this plugin.
Skeleton Horses in Vanilla & Sponge Powered servers bypass the default mob spawning gamerules.
Horses are additionally considered non-hostile mobs, so can wreck havoc with protection plugins.
This plugin has 2 mechanics.
The first is that when doMobSpawning = false, Skeleton horses will no longer spawn naturally on lightning strikes.
Secondly, it introduces a new gamerule, removeSkeletalHorse.
removeSkeletalHorse = true will remove all skeletal horses & their passengers when the chunks load.
To enable, do /gamerule removeSkeletalHorse true