At MultiSite Network Update “Can’t Resolve host”, override and continue updating

I’d say that’s not possible to hook into that…

Here’s the relevant part from /wp-admin/network/upgrade.php:

$blogs = $wpdb->get_results( "SELECT * FROM {$wpdb->blogs} WHERE site_id = '{$wpdb->siteid}' AND spam = '0' AND deleted = '0' AND archived = '0' ORDER BY registered DESC LIMIT {$n}, 5", ARRAY_A );
if ( empty( $blogs ) ) {
    echo '<p>' . __( 'All done!' ) . '</p>';
    break;
}
echo "<ul>";
foreach ( (array) $blogs as $details ) {
    $siteurl = get_blog_option( $details['blog_id'], 'siteurl' );
    echo "<li>$siteurl</li>";
    $response = wp_remote_get( trailingslashit( $siteurl ) . "wp-admin/upgrade.php?step=upgrade_db", array( 'timeout' => 120, 'httpversion' => '1.1' ) );
    if ( is_wp_error( $response ) )
        wp_die( sprintf( __( 'Warning! Problem updating %1$s. Your server may not be able to connect to sites running on it. Error message: <em>%2$s</em>' ), $siteurl, $response->get_error_message() ) );
    do_action( 'after_mu_upgrade', $response );
    do_action( 'wpmu_upgrade_site', $details[ 'blog_id' ] );
}

But from that we can make a little tool to list all dead blogs.
And an option to deactivate each one^*.

^{*Copied from /wp-admin/includes/class-wp-ms-sites-list-table.php.}

add_action( 'wp_network_dashboard_setup', 'wpse_52040_network_dashboard_setup' );

function wpse_52040_network_dashboard_setup() 
{
    wp_add_dashboard_widget( 'wpse_52040_dead_blogs_widget', __( 'Dead blogs' ), 'wpse_52040_dead_blogs' );
}

function wpse_52040_dead_blogs() 
{
    global $wpdb;
    $blogs = $wpdb->get_results( $wpdb->prepare( "SELECT * FROM {$wpdb->blogs} WHERE  spam = '0' AND deleted = '0' AND archived = '0' ORDER BY registered DESC, 5", ARRAY_A ) );

    if ( empty( $blogs ) ) 
    {
        echo '<p>No blogs!</p>';
        break;
    }

    echo "<ul>";
    foreach ( (array) $blogs as $details ) 
    {
        $siteurl = get_blog_option( $details->blog_id, 'siteurl' );
        $response = wp_remote_get( trailingslashit( $siteurl ) . "wp-admin/", array( 'timeout' => 120, 'httpversion' => '1.1' ) );
        if ( is_wp_error( $response ) )
        {
            $error = $response->get_error_message();
            echo "<li><strong>$siteurl</strong><br />";
            echo '<span class="activate"><a href="' . esc_url( wp_nonce_url( network_admin_url( 'sites.php?action=confirm&amp;action2=deactivateblog&amp;id=' . $details->blog_id . '&amp;msg=' . urlencode( sprintf( __( 'You are about to deactivate the site %s' ), $details->domain ) ) ), 'confirm') ) . '">' . __( 'Deactivate' ) . '</a></span><br />';
            echo "Response -&gt; $error</li>";
        }
    }
   echo "</ul>";
}