PDf files are not ebooks but rather digital paper. As such the formatting is hardwired and controlled solely by the publisher.
As you surmissed, the only way to control display of a pdf file is to try to extract the content from the file and convert it to an editable format. If the PDF is DRM free and not too complicated (mostly text) Calibre can do a decent job. Mobipocket Creator (free at Mobipocket.com--make sure to install it as the Professional edition) does a somewhat better job (it outputs Mobi format but the conversion folder also contains a generally very nice HTML rendition).
If the pdf is very complicated (columns, tables, text boxes, graphics, etc) the only real option is a professional converter like Abbey FineReader or Nuance OmniScan that "prints" the PDF to memory and then OCR that virtual page to create an editable document file that replicates the pdf formatting.
If it sounds like a lot of trouble, understand that PDF was designed to *prevent* you from freely accessing the content in edittable/re-formatable form and does a very good job of it.