The pellets fired from the pellet launchers will indeed be moving fast compared to the starship. There aren't any high speed physical impacts. The high speed of the pellets is an inherent part of the ramjet, in that it provides the energy to compress the pellet's plasma to initiate fusion. 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.