I think Tom died of natural causes or car accident whatever. I highly doubt Michael killed him. Tom woulden't have been stupid enough to betray the family. He saw where it got too many other people. Michael and Tom had their problems but it was all in the interest of business. He was the lawyer and he advised just as he did to Don Vito and Sonny. Sometimes they disagreed but that was one of the reasons why he was an advisor in the first place, to provide his view.
Yes Michael and Tom argued but they were in fact brothers and they only way he would kill a brother is if it involved betrayal which I am convinced Tom would never do. He was smarter than that unlike Fredo.