In the story, O'Brien is exposed to several things, like Steve's script for one and his raw emotion of terror for another and his vain rationalizations for a third. It is the accumulation of all these layers of exposure to what Steve is that re-enforces O'Brien's feelings about his actual guilt and compels her to turn away.
First of all, just being pronounced innocent does not make a person innocent. It is the lawyer's job to get the client acquitted. The nasty part of being a defense attorneys is that you sometimes believe or know that your client is guilty. Attorneys don't always believe their clients.
At this point in the book, it is important to realize that O'Brien has been privy to a great deal of information--not only from what Steve has told her and the information they gathered as his defense team, but also from what she has seen him writing in the movie script. Additionally, throughout the story, Steve makes it clear that he believes O'Brien suspects him of being a monster, hence the title. The reader is also able to see the dark perspective he presents--that he himself is not sure of his innocence. The point of view in this novel is interesting, as it is technically first person, but he uses third person objective primarily for the script. It is still tinted by Steve's own opinions and therefore cannot be trusted, which is the ultimate problem of first-person narratives: they can be unreliable.
I think O'Brien was processing the possibility, however minute she made herself believe it was during the trial, that she had just freed a young man who would only make more mistakes, or worse, progress to committing crimes of his own making. The situation was far too coincidental and we see her grappling with this in several scenes--she stops her client from writing Monster over and over, but that doesn't mean it keeps her from feeling it about him privately.