But it works at anytime on the overworld map. Just tap the S key and your fleet will cancel their order and come to a stop.
welcome to the forum. ^^
this "works at anytime" only while you actually have an autopilot course set from the map. it does nothing while you're traveling by holding the mouse button in the main campaign view. that includes manually maneuvering (to avoid obstacles or enemy fleets, or to go in a search pattern around an unexplored system) while having autopilot set but disabled.
since it's often useful to have autopilot set but disabled to have the arrows to my main destination show even while i'm maneuvering manually, that is quite often the case for me. and setting a new autopilot course on the map and then immediately cancelling it to get the stop effect, aside from obviously being much less convenient than just pressing one button, is not always a good option for that same reason.
in short, i don't always have autopilot on, and i often don't want to cancel my current autopilot when i want my fleet to stop at its current position. so unfortunately, no, that is not a solution.