Following this train of thought could it not also be said that Aikido/budo is in a way a system of rehabilitation of violence, a way of training our bodies and instincts to not be given over to violence but to reform those tendancies within us and society?
Maybe, sort of. You hear this"and society" bit a lot re: aikido; personally, I don't see it except as the collective outcome of changing a lot of individuals - in other words, I don't see aikido providing a remedy for the ills of society directly, only indirectly.
Addressing the case of the individual...again, I think it's a maybe. You speak of "rehabilitation of violence", so let's talk about the case of someone who's got that predisposition, to see violence as a tool of choice, and how aikido might change that person. I'm thinking of something my sensei said once, when a student was saying that he thought that many police officers and corrections officers would like to study aikido. Speaking of his own experiences when they had come into the dojo, my sensei said that he mostly hadn't found that to be the case. "They like to dish it out, but they don't like to take it," is how he put it. I don't think that's an indictment of police and corrections officers, so much as an observation about human nature. Many people don't mind dishing it out, but fewer are willing to embrace what it's like to be on the other side of the exchange - and some people in positions of authority have more leeway than the rest of us as far as which role they get to choose in life.
So a person comes into the dojo, whose tool of choice is violence - what does the dojo have to offer to inspire them to change? It offers them other tools, sure, but until they can see the problem as something other than a nail, they're going to think the hammer they've already got works just fine.