Mary's right, actually. Apparently, Pirates lost a lot of plot on the cutting room floor because the movie was so long already. One or two of those scenes were ones that explained the whole deal about the Flying Dutchman curse and how it should affect Will.
So, I don't think one should really blame the writers. Or even the director really. I believe it's the studio that has the final say. And as we FoLCs have all too good reason to know, most of our favourite shows/ movies would have fared a lot better if the studios had kept their noses out.