Wordpress - InDesign to WordPress workflow

Afaik: There's a (hidden?) button for TinyMCE that cleans up stuff imported from MS Word. You click the button insert (copy/paste) the stuff from Word and TinyMCE should do the rest.

Second: You can export as XML from InDesign. Why not use that? Pulling in XML data should be much easier. I'm pretty sure that you could also add a new table in DB for the XML content and pull that instead of the_content();. Adding some meta box (or just use custom fields) to upload the xml file to DB would be as easy as disabling the editor could avoid a lot of trouble.