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.
That's very true. And, much as we like to think of regular wars between families (as in Clemenza telling Michael, "Ah, dat's all right, dese t'ings hafta happen every ten years or so--lets out the bad blood"), families would much rather negotiate than fight. Wars are expensive, interfere with business, are dangerous, and enhance the omnipresent opportunities for treachery. Most of the wars we read about in real life are within families, over leadership and territories.