Are you sure that's the problem? In theory the fishbowl effect shouldn't cause a problem, unless I'm misunderstanding something, in which case the method I have in mind should work.
Forgive me if this is old news - as I said I know nothing of real navigation or its mods - but you could set the "on deck" camera fov to something like 90 (horizontal, thus giving you a vertical fov of 67.5) and add a draggable, transparent scale to the GUI, which has a height of exactly 768 pixels and is marked from 0 to 67.5 degrees, looking something like this:
Then you just align Polaris with the centre of the screen (that is, the horizontal centre - it can be anywhere vertically) and drag this scale so that the 0 mark is on the horizon, and voila.
I don't see why that wouldn't work. :hmm:
Edit: cross posted - sounds like we were thinking along similar lines.