As some previous educators have noted, the construction of this metaphor is slightly inconsistent. Willy tells his boss, Howard, that he cannot eat an orange and then throw the peel away, which of course, he can, and most people do. But Willy is in a tortured state, and it is clear to see what he really means to say. He is saying that Howard should not treat people, namely people like Willy, as if they were oranges. Willy is not an orange, and therefore it's wrong of Howard to use him up and then discard what's left of him as if he were something be consumed.
The metaphor is a commentary on capitalism and on the abuse of workers by their employers. If Willy came to Howard as a fresh, young "orange," then we can compare Howard's treatment of him to the behavior of a man who peels the skin off the orange, eats the best parts of it—the "fruit"—and then simply gets rid of what he doesn't want. Obviously, this is what is usually done with oranges.
Perhaps Willy means that it is also what is usually done with workers: the best parts of them are consumed by greedy employers, and then the empty rinds, the leftovers, are discarded, because they are not useful. Willy's comment is that, whether this is what is commonly done or not, it shouldn't be. People should not be treated like oranges, because they are not disposable material to be consumed by the system.