When I originally wanted a telephoto longer than my 55-250mm kit lens, I found a used Sigma 170-500mm with a non-adjustable aperture (stuck at f/6.3 because the lens couldn't communicate with my camera).
Testing showed that cropped shots with the 55-250mm were much sharper, with less CA, than the uncropped shots taken with the longer lens. And the keeper rate was way higher with the 55-250mm lens.
Then, when I bought a new Sigma 150-500mm I did an informal comparison with a friends 70-200mm with 2X teleconverter and found that I preferred the shots taken with the Sigma.
My opinion (for what little it's worth) is that there are too many variables involved to reduce the decision down to megapixels versus focal length. Have you thought about renting a couple of lenses and testing them in the field? I wouldn't be surprised if lens weight and auto-focusing speed became equally important considerations.
Edit: I re-read the original post. You will definitely be able to crop more with the 18mp sensor. I'd be interested in seeing your results. Also, is it practical to use a prime lens for shooting birds in flight? I would think it'd be really tough to find them in the viewfinder.