Tom was available to be used however Mike wanted, this was why he was so valuable to him. He fit into Mike structure perfectly. I dont think Tom was ever punished one time, the move to replace him with Carlo in Vages was simply a act to play Carlo. Once Mike got to Vages he wanted to use Tom as a legal front man so ue kept him away from the bs of the family until he had to lewve the family to the one man he trusted completely Tom, after this as far as im concerned he went back to consigliere.