I believe Tom did not approve of Michael's "take no prisoners" approach after the Cuba deal went down, but I also think ever the loyal soldier he stayed with Michael, and masked any disagreements. I am sure Michael continued to play him, but I get the sense that Tom may have been further marginalized as Michael moved back to New York and began selling the casino interests and getting himself involved in the "legitimate" world. Tom did not have the ability to get into mergers and acquisitions, and my guess is he played a role in selling the casinos, and then was put out to pasture with a healthy retirement package. I believe his death may have been related to all this, and of course after his death Michael was free to invite Teresa to parties, attend Andrew's ordination, tell everyone what a great lawyer Tom was and how close they were as "brothers."