Hmm, I didn't think the Captain's father was portrayed as positively in the film as you seem to think so. I got the impression that he was the last ni a long line of vicious military bastards and that the hope of the ending was that the line would be broken.

And the image of the blind creature eating the fairies is copied from a famous painting by Goya (http://en.wikipedia.org/wiki/Black_Paintings), which is sometimes seen as partly an allegory about warfare.