Inertia dampener

Oh ! You can try with Vizzy maybe. I guess you don't shoot your craft at hyperspeed "at wild" and you have a mean of targeting a body ? With Vizzy you could use the on enter planet SOI to automatically fire the ion engine ( all planets have gravity, and you said the trick works around planets ).
Alternatively, if you want to stop your ship "in space" far away from a planet sphere of influence, you could link an ActionGroup to something like : lock retrograde, fire FTL drive until speed is low. Your FTL drive should be able to stop you, because it was able to send you here in the first place.
Sorry if I did not understood the problem/how your ship works.

@zeropol maybe 800,000km/s, yep, per second lol

@zeropol sadly, it only works in planets with gravity. And by ftl travel, well, I made a ship that is capable of interplanetary travels and if the ftl drive is activated at 100%, the ship will leave out of the system in a matter of seconds and theres no way to stop because the ion engine can only keep constant speed in space while it can completely stop in a planet with gravity. I edited the xml of a specific engine so that I can travel with ease.

When you are stopped, you could deactivate the AG of the ion engine maybe, then engage your ftl ? And what do you mean by faster than light travel ? How do you do that ? Teleportation or really high speed ?

@zeropol it does work in space but stops the ship from accelerating or decelerating, keeping the constant speed of the ship itself. maybe i did something wrong idk

I did not tested this Bob9998 trick in space, but according to the description it works in space as an inertia dampener. ( tested in atmosphere, it is an insta 0m/s )
Give it a try ?