Sniper Wolf talked about what an amazing man he was and how he saved her from the desolation of her environment. Locked up, Snake cites his death as the reason why he had to leave special forces and live by himself in Alaska. Naomi also cites him as a father figure who helped finance her education and gave her a better life, cursing Solid Snake for killing him. His reputation is as "The Greatest Soldier of the 20th Century," not as madman who nearly killed us all. The LEF project is introduced as a betrayal that the player can easily compare to what they've been through with Solid Snake, and by the time the game is over, the U.S. government is no longer something the player should be surprised Big Boss challenged.
I think that's ample enough evidence.
An older plot point is not a theme. The self-defeating logic of nuclear deterrence is a theme. The 20th century emergence of Non Government Actors is a theme. Costa Rican neutrality through disarmament is a theme. The MGS series has always been about going beyond just the narrative and exploring larger ideas. All of these were new to the series.Peace Walker is to the MGS narrative what Advent Children is to VII, a rehash of old themes cause the team knows there is nothing new to talk about.
Even the point about why The Boss carried out her role - that was only one part of the story. And to clarify, Jack learned why The Boss sacrificed herself - to cancel out Volgin's destruction of the R&D site and avert a nuclear standoff. But that explained nothing about why this woman who gave her body and her child to her country, only to be betrayed by them in the Bay of Pigs, the first space flight, and presumably other incidents, would continue fighting for them up to that point in 1963. The tapes revealed later on in the game give the answer, but there's still a lot of deciphering and deeper meaning the player has to go through to figure it out.