Yes, they should since that number was associated to Fernandez and it was his. It would be a symbolic sign of sorrow for this tragically deceased man. Every organization or sports club should do such a thing. This shows that he meant something for the organization and that he could never be replaced.
The tragic death of the Miami Marlins' pitcher Jose Fernandez is a sad loss for his family and team. Retiring his number would be one way to honor him and show respect for their team member. There could also be a scholarship named in his honor as a way to encourage young people to honor his legacy.
Jose Fernandez death was a tragic accident, and he was a great player who would have continued to do great things and he deserves to be honored. Retiring the number of a player who died is a great tradion and it is one that Jose Fernandez deserves the honor of.
Retiring a player's number should be reserved for players who have been historically transcendent on the field or single handedly altered the character of an organization through their efforts. While Fernandez was a good player, he was not a player of that magnitude and there are better ways to honor his contributions to the Cuban American community.