First of all, it IS possible to stop the ship by turning around and boost thrusting, I do it all the time. The velocity bar gets smaller until it disappears. The catch is that you have to have your ship pointing EXACTLY in the opposite direction of where you are going or you will get a sidewards motion, thats the way physics work.
Thrusters are one of the systems that cannopt be enhanced with a module, which is very sad. It might help if we had a chance to enhance them.
Just cleaned my battleship (10 module slots) it can go 1500 m/s but has brake thrust of 6 m/s²... This will take some serious tweaking until its right.
Edit: Was on wrong brnach... On beta branch it has 15 m/s² brake thrust, I can live with that.
