Yeah, I am in agreement that Magic users need a little love. They are being punished more from armor, resistances, and lower base damage than Physical is.
Does not sound as if they changed Battlestomp. As far as I remember Battlestomp was never affected by weapon only by level, STR and Warfare, because the attack gets done with your foot (stomp). And that is why a staff won't change the type of damage.
This is the case for abilities that do not require a weapon, but Battlestomp requires a melee weapon and its damage is directly proportional to the damage of the equipped weapon. E.g. when using a staff, Battlestomp's tooltip states that it scales off of Intellect, and equipping a more-powerful staff will increase the damage.
However, unlike most other weapon spells, all damage is converted to Physical, instead of using the Weapon's native damage.
It is odd that a Battlestomp requires a melee weapon, but I guess they didn't want bow users getting a long-ranged AoE Knockdown.