We saw a big change in Jeremy from the beginning of the book through the end. He was so full of self loathing that he would have gladly taken a guilty conviction for something he didn't do as a way of punishing himself. I think one of the wisest decisions Lee made in his case was to introduce him to her friends Mark and Bobby. Jeremy was so incredibly isolated and indoctrinated growing up in his church environment. He needed to meet people who he could relate to- -good people, kind people, loving people, who also happened to be gay.
I feel like his aunt is very in tune with what he needs and will make sure to provide that for him. He now has a loving, safe home. Peggy has the resources to help him heal. And it seems he already has an extended, supportive community- -Lee, his defense team, and Mark and Bobby have become his friends. I get the sense they will remain in each other's lives.
I think San Francisco was a dream because it was so far removed from where Jeremy and Sam were in Colorado. No one knew them there, and the idea of it represented a real chance to completely start over. As Jeremy begins to develop a more positive sense of self and accepts that he is worthy of the love from his new "family", I don't think leaving Boulder will be necessary for him to become who he wants to be.