This scenario was an interesting read but I see it different. In the case of a healthy patient that the doctor kills for spare parts would be akin to you being able to stop the train by pulling the switch.. but before doing so you tied a person to the other track.

In the first scenario you didn't tie anybody anywhere.

I would consider this one to be a closer analogy:

You're a doctor and you have a dying patient. This patient is dying from something operable but totally unrelated to his organs (at least, the ones needed below). The surgery for this is extremely difficult and time consuming.

5 others come in from a bus wreck or whatever. All of them require a different organ, and by the light of god, the original dying patient is a matching donor for all other patients.

The 5 other patients surgeries are easier, higher chance of success, and you can do all 5 surgeries before they die.

The original patient's surgery is complicated, takes many hours, and by the time you were done doing that surgery all the other patients would be dead.

You are the only doctor within a time-allowable distance to perform any of the 6 different surgeries.

What do you do? Let the original patient die for the organs - after all, you didn't poison him or make him sick? Or save the original patient and let the 5 die while you're in surgery?

This one is harder to answer, but seems a better analogy to the train tracks than having a healthy sleeping patient.