The kinetic energy removed maybe the same but due to the rotor size difference between a rim and the disc brake rotor the forces on the spokes are quite different. The higher forces on the spokes applied at the hub flange (set by the hub flange diameter to rim diameter) do not mean higher retardation force on the bike. I have corrected my first post on this. There is a glaring error.
As I have shown torque = force applied * diameter of rotor.
Energy in one revolution is actually work done=torque*2*pi
Assuming tangential spokes
So W.D = (braking torque)2pi = force(rotor diameter). That could be rim or brake.
The work done here is fixed. The rotor diameter is not. It's 10 times larger for the rim than the hub flange pcd ( assuming 62mm Shimano 6 bolt flanges) so the force on the spokes has to becl different. Small disc brake hubs just make matters worse.
So bringing energy into this changes nothing.
So when you apply physics/naths the answer falls out. I used to teach this subject and maths too.
The problem is you are misunderstanding the relationship between torque and energy.