I wish the US had offered whistleblowers reasonable plea deals and they had taken them. Unfortunately that's not the world we live(d) in. The US pursued a policy of vindictive and extralegal punishment against "enemy combatants" that made a lot of people doubt whether they could get fair treatment.
Plea deals aren't a solution. No matter how reasonable.
This agreement itself is a plea deal, but involves the agreement in principle that Assange has committed a crime by publishing this information. That in itself is an enormous problem for people seeking out government wrongdoing.
Yeah, it's not at all clear to me that Assange did anything illegal and if he was offered a deal 12 years ago he probably would have rejected it. But Snowden and Manning definitely broke the law and I don't think it's a good look for anyone involved to have Snowden being a fugitive and cause celebre in exile for life.