Long thread so perhaps it has been mentioned so far, but the first successful smallpox vaccine developed by Edward Jenner was done in stark violation of modern medical efforts. He inoculated a child with cowpox to test his theory that cowpox exposure would immunize someone to smallpox. Smallpox was one of the more virulent diseases of its day and Jenner using an unwitting child as his test subject is a prospect most physicians nowadays would consider horrific. In some cases the cowpox inoculation did kill its patients, though due to shoddy medical records of the time other circumstances might have also been at work. Yet Jenner's work likely saved hundreds of thousands of lives, if not millions, with his vaccine. The cowpox-smallpox vaccine is in fact where we get the word vaccine. If it hadn't been for Jenner, not only might it have taken many more years for humans to discover how to vaccinate (germ theory wouldn't be developed for decades), but smallpox would have killed many people who survived smallpox outbreaks because they had been inoculated with cowpox. It was extremely controversial in its day, but (at the time) General George Washington ordered his troops on some occasions to receive cowpox inoculations, as even before Jenner, it had been observed (mostly by farmers) that those who had contracted cowpox were immune to smallpox. During the 18th century, war caused death more through disease than by death on the battlefield and smallpox was a major culprit. Numerous American Revolutionaries survived smallpox outbreaks that killed French, British, German, and Native American combatants during the American Revolutionary War.
That is the best example I can think of for ends justifying means. Of course medical science has advanced significantly since then to the point where we don't need to use humans as test subjects for these things to the same degree, and modern medical ethics requires permission from the patient. Nevertheless, at the time, with limited scientific medical knowledge, Jenner gambled on his patients' lives and humanity was the real winner. It is still important to remember however that Jenner was experimenting a hypothesis on human subjects, usually without their knowledge. And there were a great many medical practitioners in the day who acted the same on such hypotheses which turned out to be quite wrong. So are the means only justified when the ends are favorable?
