how to update a field created with field_create_instance
You can use a combination of field_info_instance() and field_update_instance():

// Load the instance
$instance = field_info_instance('user', $field_name, 'user');

// Make whatever changes you need to, e.g.
$instance['settings']['user_register_form'] = 0;

// And save it again
field_update_instance($instance);