He's making the argument that there exist certain documents that are "better left confidential", and that those documents "eventually make it out". Both statements are highly contestable, and I've offered a fairly extensive source by a Pulitzer prize winner to contradict those points.
His final statement is ironic. We're talking about a man (Manning) who risked his life to uncover information that the government tried to conceal by spreading misinformation. The existence of misinformation about Manning's own story is nothing if not ironic. It's not an insult - to Obama, perhaps, but not OP - and my apologies if anybody took that way. However, taking the time to look me up on Twitter just to call me a 'prick' certainly doesn't offer anything valuable to the discussion and does nothing to keep the level of discourse on HN high.