There are any number of conflicts within the criminal underworld. If they were all resolved by violence, there would not be any criminal underworld. Most are resolved through negotiation. Tom was made for negotiation. However, his murder credentials are quite in evidence. He was in on everything that Vito that resulted in harm to people and Vito harmed alot of people.
Most of the wars we read about in real life are within families, over leadership and territories.