First, the article specifically says how the government WILL smear. That means he knows they haven't yet done most of the points but is saying watch out for them in the future.
"It is entirely legitimate to challenge Snowden's grasp of what NSA was doing". Obviously he doesn't understand the secret programs but neither does the general public because, guess what, those programs are kept secret.
"It will be alleged that the domestic surveillance is legal. NOT PROPAGANDA." Maybe this is not propaganda but it's irrelevant to the case at hand. If it's unconstitutional, it's not legal. But the courts have not been allowed to rule on whether it is unconstitutional or not.
"It will be alleged that what Snowden did was wrong. NOT PROPAGANDA". I think the point is the administration will want to move the focus from investigating themselves to investigating him.
He leaked something that hints to the government doing unconstitutional blanket surveillance of their citizens.
Let's investigate that and leave Snowden's life or level of understanding out of it.