It is accelerateing towards the station. The overall speed of my ship is slowing but as i pitch, the ship gains speed in the new direction ot wasnt previously moving in, and i have not set the throttle to tell it to do so. It should slow to a stop and not change direction as i pitch. And i should just turn to look at the station as i fly past it and stop.
Right, have looked at the video, let's sort this out. This is working as designed.
Let's talk straight lines to start with. In FA on, you don't directly control throttle, at least not in the sense of the thrusters. You set a desired speed. FA takes care of that, by applying front and back thrust. If you set it to a desired speed above your current speed, FA applies forward thrust until the desired speed is reached. If you set it to a desired speed below your current speed, FA applies a reverse thrust until your desired speed is reached. In the video, you haven't set the throttle to zero, you've set your desired speed to zero. FA off is applying thrusters to reduce your speed. You can see your speed reducing after you've set the desired speed to zero. This is because you will carry on at the same speed unless a force is applied. FA uses the thrusters to apply that force.
So that's one part of FA.
Now let's cover three dimension and turning. As well as matching your desired speed, FA is also designed to match your current speed with your direction. This is to make your ship handle more like a plane. So, as you use your directional controls, FA converts that into a rotation of the ship and a directional thrust, in order to try and maintain a matched speed and direction. It can't always do that completely, hence drift, which is to say that the ship's direction of movement lags behind it's orientation.
So in your video, all is working as it should. You fly towards the structure. You then select a desired velocity of zero. FA starts reducing your speed. You then use your directional controls. FA then does both things discussed above, to whit, it applies thrust to reduce your current speed to the desired speed, and it also applies thrust to match your current speed with your orientation.
What you seem to be asking for is for FA not to match your speed to your orientation. This however is core to the flight model. While it might make more sense to you, it doesn't make more sense in general, as FA is there to give the style of flying in question. And changing it would be a big change which would impact on everyone who ever flys with FA on.