You can use a small trick here, just remove the front translation keys of the ship, by front translation I mean is the direction in which the ship is moving, it can be X axis, Y axis or Z axis (as you said that it is flying so I am assuming that you must have animated the translation and rotation values), so that you now have the rotation and up and down movement of the ship.. But pls save the original version of animation.
Now try the same method as you did by creating an emitter at the front of the ship (but this time i'll suggest you to use the curve based emitter) and simulate the fluid for the required frames.. (Or you can also make cache...)
What you have now is the simulated fluid layer which is behaving well with your ship's rotation, ups and downs and also respecting its surface.. Now bring in the ship with the original animation and parent this fluid container with the ship.
You can render this layer and comp it in rest of the clouds in a compositing software...
If you are still not satisfied with the results then you can use a particle based fluid 'AfterBurn', its easily available on creative crash.