Muh Dude Protection never gave you protection from spells. It does however take the fireballer out of protection if they cast an offensive spell. Note these did give retals as if it were an attack
This is by design to allow Magic users to keep up with Kingdoms that are pure army oriented.
Example, An elven army, even at its peak, cannot keep up with a Dwarven army of a similar size, however if the Elven army casts Enough (or a big enough) Fireball(s) to destroy the Dwarven population creating abandonment of troops, the Elven army can win the battle.
Protection should not stop this, especially if every offensive spell has retal rights.