I would hardly describe the deal as friendly. He already did 5 years in a prison that was worse than where he would have stayed in the US. Also, there was a bunch of legal uncertainty over the case given the 1st amendment concerns. The government would rather take a guaranteed conviction than potentially lose. Uncertainty is the same reason the government offers people a better plea deal after they get a mistrial or some evidentiary thing goes in their favor. Also, there are literally drug kingpins who sold thousands of tons of drugs and ordered executions with lower sentences than Manning. Her sentence was unfairly high to begin with, which is part of the reason it was commuted.

You seem to have the impression that leakers are getting sweetheart deals. In actuality you have people like Reality Winner who got five years for leaking information that was pretty much already public. Natalie Edwards getting six months for the FinCEN Files is probably a little low. I am incredibly skeptical that given the number of news organizations with access to the documents that they remained private and that no one was tipped off. But she was actually doing it in an effort to put pressure on Russia!