I think the problem is that the sentence "he is dying" can mean many different things:
He has cancer, and he has only months to live.
He was just shot, and he has only minutes to live.
He's not breathing, and he has only seconds to live.
In fact, if someone says "So-and-so is dying," a common follow-up question might be, "How long does he have?"
In the sentence "Who saw him die?", the word "die" is being used in the sense of "to stop living". In other words, the question is asking who witnessed the moment of death. It could be interpreted to mean "Who saw him in the act of dying?" in the literal sense of "the act of dying" as a near-instantaneous process.
If I were to ask, "Who saw him dying?", I would be asking who saw the person while they were dying, even if they weren't there at the moment they died.