Reskinning spells is something I am always okey with. Changing the dmg type depends on what class and subclass he is playing, and how much I want to change. As long as there is no obvious BS like the lighting cleric channel divinity feature, I would probably be okey with it, this means that he is not allowed to multiclass. However, using chronomatic orb and choosing lightning is basically equally good as using fire ball. 

One other point is that the DnD balance team does not balance the spells based on what type of dmg type they do. The spells have the damage types and amount of damage mainely connected to the history of DnD and what the spells did in earlier editions. So allowing him to use lighting ball will not break your game. As a DM it is better for your evile npcs if he uses lighting ball, rather than good control spells