Do Unto Others...

I've been thinking about the ethical theory of Utilitarianism. I vaguely touched on it for a project for school but was unable to flesh anything out. Following are some of my thoughts.
The founder of Utilitarianism is Jeremy Bentham. He lived in England in the mid to late 1700's. This was the period of the Enlightenment. His godson was a man named John Stuart Mill. Mill continued writing and defending Utilitarianism after the death of Bentham. Utilitarianism focuses on happiness. It had come under fire as a theory of 'swine', due to the focus on pleasure and satisfaction. Mill qualifies happiness as a level of pleasure above that which a beast could experience. He calls happiness utility and qualifies it, writing, "...we may refer it to the love of liberty and personal independence...but its most appropriate appellation is a sense of dignity." This seems to be an individually focused happiness, but, in fact Mills goes on to further qualify utility as that which is best for the larger whole. When it comes to conduct the standard for determining one's actions, "...is not the agent's own greatest happiness, but the greatest amount of happiness altogether..." In other words, the best and necessary action is the one that benefits the largest amount of people. I feel that Mill deconstructs his entire theory in the closing of his Utilitarianism: "As between his own happiness and that of others, utilitarianism requires him to be as strictly impartial as a disinterested and benevolent spectator. In the golden rule of Jesus of Nazareth, we read the complete spirit of the ethics of utility. To do as you would be done by, and to love your neighbour as yourself, constitute the ideal perfection of utilitarian morality." The problem is that in order to serve the greater good, oftentimes individual rights are sacrificed. For example, a person who commits an assault against another is imprisoned in order to protect society. The liberty of the offender is impinged in order to serve the greater whole. This is the theory of Utilitarianism in practice. If you are doing unto others as you would be done then you would not imprison anyone, lest you wish to be imprisoned. So, the utility of the whole is not served. It is in this way that the theory is deconstructed. Let me add one more illustration to my argument. I am relying on the writing of Bernard Williams in his, A Critique of Utilitarianism. Suppose there is a man who is traveling in the rain forest in a remote part of a South American country. He stumbles upon, quite by accident, a small tribal village where there is occurring a terrifying scene. A couple of soldiers belonging to the government of the country have twenty villagers lined up, all of them looking quite terrified. After explaining that he is merely a botanist who is off course and has mistakenly arrived there the man is advised by the soldier that he may participate in the killing of these villagers. He further informs the man that it is a honor to have a foreigner as a witness and participant in the killing of what he considers 'rebels.' In order to honor the occasion of his presence, he will allow nineteen of the twenty villagers go free if the man will shoot one. If the botanist refuses to kill one villager, however, the soldiers will kill all twenty. What is this poor lost botanist to do? Can he apply an ethical theory that can not even stand upon its own standards? It is easy to see that Utilitarianism is a non-theory because it can not be applied consistently. It is simply impossible to treat all others like you would want to be treated and serve the larger whole in all situations.