In the early to mid 1980s I read a short story about a ship pilot who was forced to use an emergency teleport. As I recall, the pilot did everything possible to avoid using the teleport because the teleport didn't actually teleport anything, per se. What it did was map the original body and create a new body at the teleport terminus. The result was that the original pilot doesn't actually go anywhere but, instead, died a grisly death.
The focus of the story was the psychological effect using the emergency teleport had on the pilot, both upon the original before using the teleport and upon the duplicate, knowing that he was a duplicate and that his original person never got off the ship.
Note: The fundamental plot may be identical to "The Fare," mentioned in this post. However, I distinctly remember the pilot and the psychological anguish over using the emergency teleport, so I'm 98.5% sure it's not "The Fare."