This is a discussion topic for the Ore project, DisableSkeletonHorse. View the full project on Ore for downloads and more information.
Special thanks to Pixelmon Harmony for commissioning this plugin, and allowing it to be publically released.
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 the gamerule 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
API 4, 4.1, 5 -> V1.0.0
API 6 -> V1.1.0