You just have to give up in order to realize that this can be done rather easily:

from distutils.command.install_headers import install_headers

class modified_install_headers(install_headers):

  def finalize_options(self):
install_headers.finalize_options(self)
self.install_dir = \
    os.path.join(os.path.split(self.install_dir)[0],
                           'Scientific')

setup( ... , cmdclass = {'install_headers': modified_install_headers})