Don't see it myself...
Even worse case at the moment where we come out now - that single frame where we exit the hyperspace cut scene and then re-enter normal gameplay. If instead a one second transition effect was added so we continued in hyperspace but with:-
1) The destination star delayed to be zooming up towards us along with the starfield coming into vision.
2) The hyperspace effects blending out.
So in effect rather than hyperspace ending in a single frame, and next frame a load of visual queues telling us, "oh that cut scene has ended." Instead we get a quick blend to stop that single obvious jarring transition.
I'd envisige if the background star field could be rendered and blended in very slightly zoomed in to give yet more visual queues of speed, that would really disguise the transition. ie: So over the course of 1 second you'd see the background star field appear, and very slowly/slightly move/zoom towards you, before coming to rest in their final positions where you'd then regain flight control.
Note: Again the idea isn't to make hyperspace take any longer, simply blend in the hyperspace cut-scene to the system arrival to it looks more natural/seemless. It's simply a matter of stopping all those visual changes happening in a single frame