It occurs to me that we'll have a new problem- ships that run out of fuel on an "escape trajectory"- that is, ships that drift out of system. Will they eventually end up in a distant system? Be presumed lost? When? (any speed above ~42 Km/s will escape solar orbit)
Further, will there be any safety measures to prevent orders that might lead to that? It might be nice to be able to place a standing order on all ships to stop accelerating and break if relative velocity ever reaches remaining Delta-V.
Indeed, ordering a crew to ignore "red lining" might even require a morale roll.
On a related tangent, will ships have to decelerate when approaching planets? Certainly atmospheric breaking and gravitational breaking can do a lot, but if it's late game and a ship with no fuel tries to land at 0.23 C, I get the feeling there should be problems.
Beyond that, if you can stop instantly at a planet, then a ship in an asteroid belt has nearly twice the maneuverability of a similar ship outside of it- instead of decelerating, then accelerating the other way, the ship needs only adjust course to a nearby body, stop at it, then accelerate away.
All that said, gravitational flybys, braking, and slingshotting are an essential part of traditional space travel. It would be interesting to include it, though simplification would be required. Avoiding actually doing a lot of math, you could make a ship leave orbit with a certain percentage of its arrival velocity depending on the mass of the ship, the mass of the body, the arrival velocity, and perhaps pilot skill.
In such a system, a fighter swinging by Jupiter could come to a stop or get 1000% speed, while the death star might only gain or lose 1-2% of velocity swinging past an asteroid.