before his revelatory moment, he's still human. The conflict of the film is between the two identities of Jason Bourne before and after the amnesia. Why did he choose to join Operation Treadstone? In what sense does he no longer identify with that he, and can have the freedom not-to?

To cast the good and the bad into the human and the machine is too simplistic and normative, and isn't justified by the film. The film is the utter alienation of this self-relation to his previous self which is both not-him - insofar as he doesn't recognise his old actions, is disgusted by them, can't remember them - and is-him, in the sense it was the same body, and 'identity', which he cannot escape. This new-him is still stuck in the consequences of the old, both in terms of being 'wanted' and his ingrained training. Indeed both sides of the divide produced by the amnesia contain a mass of violence and killing, it seems suspect to parse that and justify the new-him, though your post doesn't develop that antinomy being mostly synopsis. For me all films of the series suffer a purely negative, antithesis, characteristic; the question of identity, and the radical freedom of creating anew is delayed indefinitely due to the inability for Bourne to define himself in any other way than against the past.