The experiments Alice describes being conducted on the inmates at Arkham would be very illegal in reality in this century. Also, it's illegal to commit someone to a mental institution against their will without a court order, which Jacob and Kate can't have gotten because they're keeping the fact Alice is related to them secret and she had no trial.
While tied up and just punched in the face, Julia said she'd been punched 9 times. The next day, when talking to Sophie, she appeared to be perfectly fine with no visible results from the large thug's punches.