I think implementing terminal velocity would be beneficial to this system.
Not only is it mathematically reasonably simple, but it's also going to work as a rudimentary atmospheric friction model.
The maths of it goes like this:
F = -G - kv^n
where
F is the resultant force vector
G is gravitational force (weight) (G=-mg)
k is friction coefficient (determined from values such as shape coefficient and air density)
v is velocity
n is the exponent for velocity, which varies depending on the speed itself, but for a rudimentary system it's more or less safe to approximate that n = 2. Basically this number increases as velocity increases, but that makes the equation needlessly complicated. Usually the friction coefficient is experimentally defined and ranges from zero to 1; for most FS2 ships I suppose it would range between 0.5 and 1.
As for solving the equation, using n = 2:
F = dp/dt = m dv/dt
m dv/dt = -mg - kv^2
dv/dt = -g - (k/m) v^2
1 / (-g - (k/m)v^2) dv = dt || Int(..)
v t
∫ 1 / (-g - (k/m)v^2) dv = ∫ dt
v0 t0
...
v(t) = - (√g√m / √k) * tan ( [√g√k) / √m] t - arctan [(√k / √g√m) v0] )
And there you go; of course, this is a simplified equation where movement is limited to one axis. If you allow movement in all three dimensions, then you have to formulate the air friction so that it's always vectorized against the velocity vector, while gravitational force always pulls "down" (in homogenous gravity field approximation, that's the same direction everywhere in the game world).
If you can hook accelerations into the engine directly instead of velocities, that would make things easier still, since solving the diff eq wouldn't be even necessary, you could just plug the forces divided by mass into the engine and it would apply the accelerations to objects.