That's not why Tom was a bad boy.
He was bad because he was a traitor.
There's no greater offence than selling out your own people/country. What made it worse was the was the son of a high ranking, well respected Admiral
When things got to tough for him in Starfleet he quit but he didn't just quit, he turned his back on the Federation by doing so. He joined the Maquis. After he joined the Maquis, he turned on them and sold them out to Starfleet.
He couldn't be trusted and wasn't welcomed by either side.
He was a traitor to his father and to his "country", he was also a traitor to the terrorist/freedom fighters he joined.
People who are traitors to the government/country normally don't get let out of prison to redeem themselves. They're usually are up for execution.
And yet he has such a baby face. Especially in last few seasons when he got a bit fat.