Here is my snippet to declare views templates stored in the "template" folder of my "custom_module":

/**
 * Implements hook_theme_registry_alter().
 */
function custom_module_theme_registry_alter(&$theme_registry) {
  $extension   = '.tpl.php';
  $module_path = drupal_get_path('module', 'custom_module');
  $files       = file_scan_directory($module_path . '/templates', '/' . preg_quote($extension) . '$/');

  foreach ($files as $file) {
    $template = drupal_basename($file->filename, $extension);
    $theme    = str_replace('-', '_', $template);
    list($base_theme, $specific) = explode('__', $theme, 2);

    // Don't override base theme.
    if (!empty($specific) && isset($theme_registry[$base_theme])) {
      $theme_info = array(
        'template'   => $template,
        'path'       => drupal_dirname($file->uri),
        'variables'  => $theme_registry[$base_theme]['variables'],
        'base hook'  => $base_theme,
        // Other available value: theme_engine.
        'type'       => 'module',
        'theme path' => $module_path,
      );

      $theme_registry[$theme] = $theme_info;
    }
  }
}

You should be easily able to fork it override an existing theme instead of adding a new one. Hope it helps someone.

This is the code I use to declare a view template stored in the template folder of a custom module.

/**
 * Implements hook_theme_registry_alter().
 */
function custom_module_theme_registry_alter(&$theme_registry) {
  $extension   = '.tpl.php';
  $module_path = drupal_get_path('module', 'custom_module');
  $files       = file_scan_directory($module_path . '/templates', '/' . preg_quote($extension) . '$/');

  foreach ($files as $file) {
    $template = drupal_basename($file->filename, $extension);
    $theme    = str_replace('-', '_', $template);
    list($base_theme, $specific) = explode('__', $theme, 2);

    // Don't override base theme.
    if (!empty($specific) && isset($theme_registry[$base_theme])) {
      $theme_info = array(
        'template'   => $template,
        'path'       => drupal_dirname($file->uri),
        'variables'  => $theme_registry[$base_theme]['variables'],
        'base hook'  => $base_theme,
        // Other available value: theme_engine.
        'type'       => 'module',
        'theme path' => $module_path,
      );

      $theme_registry[$theme] = $theme_info;
    }
  }
}

You should be easily able to fork it override an existing theme instead of adding a new one. Hope it helps someone.