The batclan starts out by deciding to harass a guy who, according to the legal system, has legitimately paid his debt to society. At this point, they had apparently decided to scare him and make him 'fear' them, with no evidence that he intended to return to crime.
Yes, he ripped off a guy for a hundred bucks, and they were right to step in there. On the other hand, Cass then went on to assault him after he had been *kidnapped at gunpoint*, and that seems to have been the last straw. Nice work, Batfamily.