I think it would be intuitively helpful if using either the thrust or the stop command cancelled any in-progress docking maneuver. Any key held down before the docking command, or released during docking, would have no effect, just starting a new command.
The rationale here is:
(a) "take evasive action" is an intuitive panic reaction to, amongst many other things, find you are docking somewhere you don't want to be.
(b) if you actually want to dock, there is no rational reason to be using manual thrust
(c) on a personal level, every single *&% time I want to cancel out of docking, I find myself desperately thrusting against the dock ports gravity before I remember the cancel command
Thrust/Stop should cancel docking
This would be a good idea, except for one catch: There are times when you need to dock at a moving thing (CSCs for example) and sometimes Transcendence can't get your ship in the right position with the object you're docking with moving about. For CSCs, it's not a big problem because after a time we'll get into the right position, but in some mods where moving dockable objects are added, these things can be almost impossible to dock with, except if you use the manual thrust. Flying in circle while being in the docking process helps in these cases.
Yes, look at my avatar, I have a wyvera type ship.