What does the pilot want in the Tom Godwin story "The Cold Equations"?

Tom Godwin's story "The Cold Equations" is a science fiction story about a girl who stows away on a supply ship bound for a planet called Woden.
Like any good science fiction, the story derives its drama from a realistic and believable situation that involves science. The story is set in the future when interplanetary travel has become frequent and mankind has begun to colonize other worlds. 
The story takes place inside a space vehicle called an Emergency Dispatch Ship, or EDS. These ships carry a relatively small amount of rocket fuel that is carefully calculated to be just enough to get them to their destination and back. When the girl stows away in hopes of visiting her brother on Woden, she adds extra weight to the ship. This will cause the ship to burn more fuel than expected, which would lead to its destruction.
The ship's pilot, Barton, discovers the stowaway and contacts his superior for instructions. In fact, Barton knows that he is supposed to jettison the girl to save the ship and its supplies, but he is hoping that his commander will give him permission to try to carry out the mission with her on board. Instead, the commander says this:

So you called me in the hope I could do something? I'm sorry--I can do nothing. This cruiser must maintain its schedule; the life of not one person but the lives of many depend on it. 

So what Barton wants is to try to save the girl. What he actually does is follow orders and jettison her to her death in space. You possibly also argue that what he most wants is to survive and stay out of trouble with his superior, since he is unwilling to defy his orders.