How long are you playing, if I may ask? I had trouble at first too, but after a day or so the reversed controls became quite easy to handle.
To determine your movement vector and speed, it's very helpful to look at the floating bits of dust everywhere on the battlefield. They are static and offer a good orientation point.
Uiing the pause function helps, too.
It's not the reversed controls that make it hard, it's using weapons and moving simultaneously since you have to hold down the key until you're floating in the direction you want which means you can't really fire the non auto weapons too well. I find that with small ships it's hard because you usually overshoot with the rotation, and with the larger ships it's the time it takes to spin. The thing that would make it easier to control is where you want the vectors to be, and the game tries to move to those vectors as quick as possible. With the fancy weapon overlay it would be nice to see the vectors involved too, if I recall correctly there was a video which had them
showing to display some sort of AI which avoids missiles.
I also prefer to not use the pause as it makes the game significantly less fun, it's less of the heat of the moment and more strategic at that point.
Theres also some trouble with large ships and not having enough zoom space since your weapon range starts to become rather long, and you can't snipe without panning the camera somewhat which in turn screws up your navigation ability.
I've had starfarer for around 2 years now, and been playing it on and off but I've always had trouble with this.