Tom was basically a good guy (relative to typical Mafia hoods) caught in an unscrupulous situation. His virtue was loyalty, but not to Michael; it was to Vito. Tom served Vito's son, he was Vito's adopted son, he was Michael's brother, and he was Vito's and Michael's partner in crime. Those bonds were almost impossible for Tom to break. By leaving Michael, he probably felt that he would be disloyal to Vito. His affair was probably to help relieve the stress of his moral conflict. His efforts (?) to find other employment were a muted attempt to resolve his moral conflict by removing himself from his environment. Of course, the vice-presidency of the hotels was also a cautious attempt since they were still part of the Corleone enterprises.