In fact, the Ends are the only thing that justify the Means.
Here is a trustworthy saying: "Desperate times call for desperate measures."
I haul my ass out of bed each morning, crawl into the office, and put in a good eight- to ten-hour day for The Man. What could possibly justify such exertion, such servitude, such sacrifice? Oh, that's right: I have goals. Food, shelter, entertainment. My Ends are the opportunity to build a better tomorrow for myself and my family. They fully justify the job, my Means.
Firefighters go to great risks, running into burning houses. Where they can afford it, they spend huge amounts of money on expensive safety equipment. What could possibly justify all these risks and expenses? Could it possibly be the Ends? The rescue of human beings from deadly fire? Could it be that the Means, sending healthy individuals into mortal danger at great expense, is totally justified by the Ends, saving others from mortal danger?
Thousands died in the carnage at Normandy, when the Allies invaded Europe from the sea, and began the long counterattack that would rescue many nations and millions of people from Hitler's rule. Who would say that such an End to Nazism didn't justify that great sacrifice, and more if necessary?
The Ends justify the Means. Only the Ends justify the Means. But not every goal justifies every method of achieving that goal.
What we come to is this: An End may be good or bad. If it is a bad End, then no Means to it are justified. Nazism doesn't justify diplomacy and negotiation any more than it justifies war. And even if the End is good, it doesn't justify all Means to that End.
So the next time someone tells you that Ends don't justify Means, remember that Ends are the only things that justify means. Then judge both Ends and Means accordingly.