Starsector never implemented a simple engine angle check.
It really shouldn't be that hard to have the game check engine angles and treat all pointing back/forward as main engines/retros and the rest as manouvering thrusters and fire them accordingly.
Basically, since 0° is forward, anything from 315° - 45° would be retro thrusters, from 45° - 135° right manouvering, from 135° - 225° main thrusters, from 225° - 315° left manouvering.
If strafing right, fire all right ones.
For turning the ship an additional check is needed - offset from center.
So, if you're turning right, fire all RIGHT trusters that have positive ++ offset ( coordinates 20.5 and 50.8 would mean thruster is located forward right on the ship) AND all LEFT thrusters that have negative -- offset.
For turning left, you'd check the same, but offsets would be -+ for right and +- for left.
Simple to implement, but we're talking a minimal 6 new engine points per ships. I don't know how it would affect performance, but shouldn't be too bad.