The mobster kidnapping scheme could be considered chaotic good, perhaps, but his agreement to keep Beckett from getting anywhere with the investigation that angrily drove her every day wouldn't qualify as "good" to me, even if it was self-defensive.
His ongoing unethical behavior, knowing that she was constantly hurting, pushes him out of the top half of the alignment grid, in my opinion.
He was doing it to protect her. Otherwise they would've killed her.