How we cite our quotes: (Chapter.Paragraph)
Quote #1
"I honestly believed I could prevent any serious assault on you. But I can't protect you when you've done the damage."
"It was provoked."
"To the extent it was inflicted? A broken wrist and lacerations requiring sutures on a man's throat and face, and another's skull.A severe concussion, and an undetermined injury to a kidney? To say nothing of a blow to the groin that caused a swelling of the testicles? I believe the word is overkill."
"It would have been just plain 'kill,' and I would have been a dead man, if it'd happened any other way." (2.108-111)
Washburn is reprimanding anonymous dude (later Bourne) for beating the tar out of several locals on a sailing ship. Bourne says that he was defending himself: he had to use extreme violence to prevent his own death. This nicely sets up the logic (excuse?) for Bourne's violence in the rest of the book. He's always under threat of death. Therefore, even the most extreme violence (like kidnapping innocent people) is understandable and reasonable.
Quote #2
For an instant it occurred to him that someone had deactivated the scanning machinery in the elevator. Koenig. He would remember; there'd be no amnesia where Herr Koenig was concerned. (4.7)
This is a promise of revenge against Herr Koenig, the bank official who betrayed Bourne. Revenge here is also a promise of justice—and, in the novel, where everything is done in the shadows outside of the reach of law enforcement, personal revenge becomes almost the only kind of justice available.
Quote #3
Thirty minutes ago in another car he had experienced a degree of nausea when he had pressed the barrel of the gun into her cheek, threatening to take her life if she disobeyed him. There was no such revulsion now; with one overt action she had crossed over into another territory. She had become an enemy, a threat; he could kill her if he had to, kill her without emotion because it was the practical thing to do. (6.112)
Bourne here appears ready to kill the woman he's kidnapped just because she (very reasonably) tried to escape him. We eventually learn that Bourne isn't really an assassin, but if he's willing to murder innocent people simply to protect himself, it's not really clear how being an assassin would make him morally worse. Murdering innocent people is murdering innocent people, after all. The idea that Bourne is a good person with whom we should sympathize—pushed later by Marie, and by the novel as a whole—seems undercut by this passage.