Two of the three crew members are killed, one of whom dies later in hospital.
There are initially three people, and two of them are dead. Let's call them A and B. Let's say B dies later. Then the sequence of event goes like this.
Plane crashes -> A dies -> B dies in the hospital.
To describe this sequence of events, I would say:
Two of the three crew members were killed; one of whom have died later in hospital.
because there's a need to differentiate the time of each death, but I'm not too sure if I have achieved it correctly. I would argue that the first sentence is wrong because the later clause indicates the present, which clearly does not make sense.