Those thugs beating up Caleb Mir are not Federation. They work for the something or other empire. The judge who sentenced Caleb’s mum resigned from Starfleet the next day, saying it was the worst mistake of her career and she can no longer work for an organisation that expects her to do things like that. 20 years later, Starfleet admits she was right, and offers her a job as Chancellor at Starfleet Academy, teaching the next generation to be better than the last one.