Rainboe,
What the aircraft is doing relative to the ground has no bearing on an aircraft's performance due to inertia. Inertia affects an aircraft in relation to the difference in wind velocity relative to the aircraft in its present position compared to where it was a moment ago.
Using the 200 knot jetstream example - when the aircraft is traveling perpendicular to the jetstream it is traveling at 200knots sideways relative to the ground yet the rudder will be in exactly the same position as if heading directly into the jetstream. Given the same air pressure, temperature, aircraft weight, power and configuration the aircraft will fly at the same indicated airspeed whether flying into or against the jetstream.
However if you pass through a significant wind sheer where the wind is perpendicular to to the aircrafts flight path the aircraft will yaw and some rudder use will be required to maintain both the heading and track.
It's like the turning downwind myth where if you turn downwind an aircraft will lose airspeed because of inertia. When you turn downwind when you are climbing close to the surface you are generally climbing into faster air - which once you are past perpendicular to the wind direction will result in a tailwind sheer - which will cause a loss in airspeed and performance. Generally when you are turning downwind at low level there is also an obstruction in front of you - the further away from the obstruction you are the faster the wind speed - a tailwind sheer again. Add the fact that many pilots skid or slip because of the illusions that are generated when flying close to the ground in wind will result in more drag and a reduction in airspeed.
That's the way I see it anyway.