Newton's third law doesn't necessarily mean the same amount of work is done on both objects. For instance, consider a block attached to a spring attached to a wall. With the spring initially compressed, it does work on the block as it moves away from the wall, but the spring does negligible work on the wall because the wall is not moving. Substitute pressurized gas for spring, bullet for block, and rifle for wall. An added complication is that the force on the bullet is actually due to gases in the barrel, so if the gases are accelerating then the rifle will feel a different force than the bullet.
The best way to analyze the situation is using conservation of momentum. Assuming the bullet and rifle are both at rest before firing, total momentum must be zero. Take .01kg for the bullet mass, 1kg for the rifle mass, and 1000 m/s for the muzzle velocity. Then .01kg * 1000 m/s = 1 kg * V_rifle --> V_rifle = 10 m/s. In contrast, the kinetic energy of the bullet is .01kg * (1000 m/s)^2 = 10^4 J versus 1kg * (10 m/s)^2 = 100 J, so I would expect the bullet to have around two orders of magnitude greater energy.
You could check wikipedia for "Free Recoil" and "Muzzle Energy" if you want to see how accurate my approximation is.