That, or a simple flag being turned on as soon as someone targets you and opens fire...
*LOAF targets me and pulls the trigger once*<Hypothetical, of course
PC:!setvar in-combat 1
*I mash the autopilot button*
PC Message: Cannot autopilot, enemies near
*LOAF decides to be merciful, backs off*
<thirty seconds pass>
PC:!setvar in-combat 0
<autopilot light kicks back on>
Combining that with a 10-second warmup for autopilot would work....
hmm, perhaps if both players disengage, and don't face each other for 30 seconds... that and autopilot would be just like it is in Freelancer, to an extent... your ship enters autopilot, orients itself towards the navpoint, you hear a scoop-closing sound(something obviously mechanical), and you get an afterburner-style thrust effect from inside the cockpit, climbing in speed until you near the target (let's say, the ship climbs in speed constantly until you get about 20k out, the fuel gauge constantly dropping(not the AB gague, perhaps an OSD in the nav screen?), and when you reach 20k out, you hear the scoops open again, and you decelerate from your full speed down to cruising speed within 10k to mark(giving you a deceleration effect by lurching the cockpit). Travel wouldn't take terribly long(I'd estimate about 3-5 minutes would be sensible, breaking off in range of obstacles, and enemy contacts), and would give people incentive to navigate around asteroids/known pirate bases(unless, of course, you were a pirate)...
Just a thought.