How to override jquery update preprocess page The objective is to exclude certain javascript files from some sections of the website.

I exclude javascript and css files in this way in the template.php file of the theme:

function phptemplate_preprocess_page(&amp;$vars) {    
  $scripts = drupal_add_js();
  //PRINT THIS ARRAY AND UNSET THE UNWANTED ARRAY
  // unset($scripts['module']['sites/default/files/js/jquery-min.js']);
  unset($scripts['module']['YOUR_PATH_TO_JS']);
  $vars['scripts'] = drupal_get_js('header', $scripts);    
}


However it seems that jquery_update preprocess is executed after template.php, so it overrides my changes:

function jquery_update_preprocess_page(&amp;$variables) {
      ...
      $variables['scripts'] = drupal_get_js('header', $scripts);       
}


The code is located in jquery_update.module

How would be the best approach to resolve this?

I would prefer not to hack or disable the jquery_update.module code if possible.

Any alternative ways to exclude javascript files that doesn't involve touching the template.php file would also fix my problem I think.
JSAlter module for D6 should solve your problem..

Project page says


  This module will not be ported to Drupal 7, because Drupal 7 core
  natively includes a hook_js_alter(). Note that the signature and when
  the hook is invoked is slightly different in Drupal 7 core than it is
  in this module.
  
  This module adds a hook_js_alter() hook that other modules can use to
  modify the javascript that gets output to the page. The module
  provides no end-user functionality, but other modules can use this
  module as a dependency. Check out the JS Registry, JS Debug Helper,
  and jQuery Form Update modules for examples.