Have you tried something like
// relationship field "Fächer"
// the key of the field "Fächer"
add_filter('acf/fields/relationship/query/key=field_5593ec53f0a0c', 'my_relationship_query', 10, 3);
function my_relationship_query( $args, $field, $post )
{
// show only pages with this special template
$args['meta_key'] = '_wp_page_template';
$args['meta_value'] = 'page-fach.php';
return $args;
}