If I understand what you want right, the important thing is not so much that the pages are cropped, but that certain parts of the pages are not converted -- and so it would be equally good just to remove parts of the page and leave them blank?
PDFedit can remove parts of a PDF so that they are completely gone, and hence don't get converted in with calibre. (I think that's an Ubuntu package so you can just
sudo apt-get install pdfedit.) I don't know how easily it handles batch removal of headers and footers, though, I've never tried.
There might be some other options; I'll report back if I think of anything else.