Old question but I just came accros a fix.
I hope it helps someone else.
Add this to your theme functions.php file
add_action( 'wp_before_admin_bar_render', 'remove_mysites_comment_link' );
function remove_mysites_comment_link () {
global $wp_admin_bar;
foreach ( (array) $wp_admin_bar->user->blogs as $blog ) {
$menu_id_c="blog-" . $blog->userblog_id . '-c';
$wp_admin_bar->remove_menu($menu_id_c);
}
}