In vanilla, chain lightning is basically only an area-affecting damage skill, like e.g. Fireball. The only thing that differs is the impact data that makes it looke like it was jumping from one target to another.
The result is that usually, your melee-followers or reanimates or atronachs are hit by the spell and thus potentially killing them.

I tried to solve that by creating certain conditions, e.g. "target must be hostile to player", which works but also prevents you to attack a peaceful target with that spell. Any ideas or suggestions? Is there some attribute that all followers/summons/reanimates that are somehow allied with the player share?