How to unset CSS class for menus in the template.php?
If you want to override a core stylesheet, add it to your theme .info file.

That way, the .active class need have no CSS rules

e.g: themename.info

stylesheets[all][] = system-menus.css



  To override a core or contributed module style sheet, it must be
  specified in your theme's .info file. Drupal overrides are cascading
  and your theme's stylesheets override any that were previously
  declared. For example, system-menus.css is located at
  "modules/system/system-menus.css". If you place a file with the same
  name in your theme's folder and add the following entry to the .info
  file, the original system-menus.css file will be ignored and your
  version will be loaded in its place.


More info here: http://drupal.org/node/263967

See also hook_css_alter for a code-based solution to remove stylesheets.