In the short term, my sense is that Raul Castro would take over. However, the Kennedy administration era CIA might eventually begin planning to assassinate Raul as well when it becomes clear that the Castro regime is not going to die with Fidel. Not sure precisely what happens if both of the Castro brothers die.
Adding some more...
From what I heard, Che started in time to.. embarass and annoy the perhaps more pragmatic and calmer Castro (before his flaunting longggggg discourses), and he was.. released for his pet guerrila projects (was it done with pression? I always wonder if he was just freed for this, with blessings from Castro, or... Castro more or less 'told him to go'.).
I am not sure about Raul and the party-state's cacciques, but Che may have annoyed them too (did he had allies, in a potential internal troubles period?), and I'd say raul may have been less subtile and more direct. Che may have been kicked away, if Raul was forced to take over after assassination and before Che left in OTL.
Heck, maybe, if the assassination was done VERY well and discretely (and there would be no real proof showing of US involvelment), Raul could be paranoid of the Che OR vice versa, and.. stuff happens.