proper way to edit drupal_page_header() I can't find a hook for overrideing drupal_page_header() in bootstrap.inc and it doesn't feel right to make changes in bootstrap.inc.

Is there another other way that I'm missing?
If you goal is only to change the Cache-Control you can use drupal_add_http_header(). According the documentation this function allow you override an existing header. If you add it in you template.php you'll able to change the header without patch the core function.