The other reason why it is hard to explain these views as inconsistent is because in the case of the trolley one has to make a split decision as to whether or not to divert the trolley, but in the case of the transplant the doctor is making a pre-meditated decision to kill. The bystander in the trolley scenario has no choice but to act.
Question 2
I think that there is a morally important difference between killing and letting die. This is because there is a difference in performing an action that has a consequence and failing to do something that has the same consequence. Killing is worse than letting someone die because it would mean actively harming someone, but when letting someone die one simply omits to save them. An example: someone is hanging off a cliff, you choose not to help them because you know that you will fall too (letting die). Someone is hanging off a cliff and you step on their fingers to ensure that they fall (killing).
Question 3
The rationale that a classical utilitarian might make in the case of the spare-parts surgeon would be that killing the one man to save the lives of the five other men would be the moral thing to do because it would be the the action of greatest utility. Classical utilitarian would calculate that five deaths are worse than one death, so in this situation they would argue that the doctor ought to kill the one in order to save the five, thereby maximizing the happiness of the greatest number of peopl