Not necessarily. Each spell has their own variable for their base spell damage yes? Just add another one, and apply a simple condition checking if the target is a player or not. If it is, it uses value A, otherwise it uses value B. They already have this for some spells, such as heroic throw with the glyph checking if it should or shouldn't silence the target.
It might be a bit of work to set it up at first, but afterwards it will be so easy to change around in the balance of the respective field without even having to consider how it would affect the other that it's not even funny.
The tool tips would perhaps become a little bit longer, having two lines in its description, one explaining the damage on an NPC, and one explaining the damage on a Player. But really, it would perhaps be confusing for some people for like one week, then they would most likely understand that it's a great and well needed change.