A nod is all Snake gives in reply to Ginko's question, but the statement makes him freeze.

It is his fault. It is. Snake should have left when Joker told him to. And even now, he could go back to himself, except... He doesn't want to leave his brother alone, even if their relationship is a mess. So this, this state, is completely his fault.

He can't convey this easily to Ginko, though. He can't usually speak for himself. It just doesn't work. He can't do it, so he simply hangs his head a little as he cleans the tongs.