I have two scenarios.
One; imagine that, at the same time as the engine of your ship is ignited, there is also a device detonated inside the ship. If timed correctly, the difference between the two would equal out, right? For now, there's one huge problem and that's making sure the aim is correct, because, if you collide with an asteroid or something, you'd just spin out of control, but if you could measure the trajectory perfectly, there would be nothing in the way of that, if space, truly, is a vacuum which could accommodate fast travel. Next, there's the slowing down. Once the blast has burned out, you would naturally slow down, but the process of slowing down an object from something in the area of the speed of light would take immensely long, but you can calculate how long you go by adjusting the strength of the device according to distance. If there is some kind of resistance in space, fine, and if not, you can fire an engine in the nose end of the ship and initiate the stopping sequence that way. If there is only miniscule mass the stopping force would have to be on a par with the start force, and, again, if you detonate outside and inside at exaclty the same time, then you won't have a problem, right? Relative to ... the sides of the "ship", your pod hasn't moved at all. In short, dead accuracy is the way to go.
Two; imagine a huge construction with several hundred stories of tunnels with rails in them, which all contained a smaller pod except the one in which you have the astronauts, and imagine also that the pods of this Matryoshka ship has springs in both ends and, when the ship speeds up or slows down, the springs lessen the impact, and reduce G-forces to an acceptable minimum. The challenge as I see it here, is not just accuracy, but sheer size, since the force of, even, a jet engine in a vacuum would be immense and, so, you'd need 100s, maybe 1.000s of pods. I'm sure that having vacuum inside the tunnels would help, since that would lessen the immediate impact, but it would make the length of the tunnels a great deal bigger.