If the objective is to be the last man standing, a ship that can out range and out maneuver another ship will always win, as long as there is room to maneuver, and infinite time. This is fine, that's just how fights work.
What needs to be done is
A : limit the amount of room to maneuver, as walt has already done in multiplayer.
B: have objectives other than last man standing. Can you imagine missile kiters winning a king of the hill match? No, they'd get shredded. Can they destroy a heavily shielded and armored ship before a time limit is reached? No, too much of their cost is invested into thrusters.
Now imagine at some point the 'standard' multiplayer match might consist of a best of 3 rounds, with a different objective each round, but you have to choose your ship at the start of the match and can't switch in between rounds. Now all of a sudden picking something as specialized as a kiter seems like a terrible idea.
Same thing if bounty hunter consisted of a variety of missions rather than a series of 1 v 1s.
So overall, while kiting can seem unbalanced in the current state of the game, I think it's a problem that'll go away by itself as the game matures, and there's no real need to implement a hard counter.