How Can I Change The Tax Query For The Main Loop For Taxonomy Archives?

@birgire answer is fine (+1 from me), however $query->tax_query->queries can contain more than one taxonomy, and $query->tax_query->queries[0] can be the query for another taxonomy.

So, if you want to set 'include_children' to false (note that it is a boolean argument) on the taxonomy ‘TAXONOMY NAME’, then you should be sure that you act on right taxonomy:

add_action( 'pre_get_posts', 'slug_cpt_category_archives' );

function slug_cpt_category_archives( $query ) {
  if ( is_tax( 'TAXONOMY NAME' ) )  {
    foreach ( $query->tax_query->queries as $i => $tax_query ) {
      if ( $tax_query['taxonomy'] === 'TAXONOMY NAME' ) {
         $query->tax_query->queries[$i]['include_children'] = false;
         // if you want to set 'include_children' to false for all
         // taxonomies than remove following return
         return;
      }
    }
  }
}