No the energy would be released in the scop system ahead of the ship. This is just fine. Fuel impacts frount of ship. This is exactly what the magnetic nozzle does. Because the ramscoop didn't remove energy from the plasma in the first place.
Magnetic fields are conservative.
Like I said, you have to look at in terms of the inertial frame of the ship. That means that the momentum of the bit of plasma has changed in the backward direction. We know the pellet has a change in momentum in the backward direction. The only other thing out there is the ship. Therefore, there is a forward change in momentum in the ship.