I believe that it wasn't a question of deserving to die. Rather, as Oli said, it was a function of "their" (i.e., Michael's) world being so different than ours. From Michael's viewpoint:

--Fredo had betrayed his brother for personal gain ("He said there'd be something in it for me"), nearly causing Michael's and Kay's deaths. His violent outburst in the boathouse showed how deeply Fredo resented his brother. It'd be just a matter of time before another of Michael's enemies approached Fredo with an offer to "finish the job."
--Though Pentangeli's recantation of his Senate affidavit made him useless as a witness against Michael, he still knew plenty of damaging stuff about his former Don. The FBI wasn't going to let him "live better than most people" on the outside without constantly pumping him for info. Sooner or later, they'd get something from Pentangeli that they could use against Michael.
--Roth was Michael's most dangerous, most resourceful enemy. Look how, despite being near death in Havana, he rebounded to trap Michael into five counts of perjury that nearly landed him in prison. As long as Roth drew breath, Michael wouldn't be completely safe.

Being a Don also impelled Michael's ruthlessness. Dons are constantly being sized up and tested for weakness by foes, potential foes, and even those close to him. Michael had to show them--yes, even Tom, Rocco and Neri--that no one, not even his own brother, gets a pass for betrayal. He also had to show that nothing could stop him from exacting vengeance--not even Pentangeli being guarded 24x7 on an Air Force barracks, or Roth being surrounded by law enforcement at an airport.