The Global Weather is what makes the lightning Rods work, so a Weather Controller really seems like one of the things that can do Thunderstorms.
Here a short incomplete List of things that will work for cheesing the Lightning Rod:
Forestry Rainmaker (though Rain is less Efficient than Thunder)
The aforementioned Weather Controllers (if they actually globally change Weather)
Mystcraft Weather Pages, so you could place a Lightning Rod in an eternal Thunder/Rain Age.