If the end justifies the means, then that means everything everyone does from now until the end of time is completely inconsequential since at the end of time the end will be the same regardless of what everyone did.
Why does one particular end matter more than other ends? If I end someones life to save the life of someone else for now, what does it matter when the one who lived eventually dies of old age? At that point both are dead, and this new end is the same despite your efforts.
The moment is what matters, what one does in this ever moving moment. If you commit an evil act now, for whatever past you remember or future you imagine, you have done an evil act and that's what matters and should be judged.
Good and evil are not additive or subtractive. Someone who murders one life and saves one life, is not the same as someone who neither kills one life and saves another. Someone who takes a life to save 10 others is not good, they simply believe they have the right to decide who lives and dies.
Anyone can justify anything. Millions of lifeforms die so that I live, and I go on living. Pain and pleasure are inextricably linked, as are good and evil, and life and death. Every child born brings pleasure and pain and death and life and good and evil, and they'll be balanced accordingly and all remembered in time and then forgotten.
True perceived morality and justice is just a matter of personal reality and attachments. The murder of someone important to you will undoubtably seem despicable, where as the million deaths of those who are nothing to you is just par for the course. Which is hardly surprising. We are self-centered by virtue of our existence, we have a first person perspective.
From a personal perspective, the ends do justify the means. I'll make a sandwich in order to eat it, but I wouldn't bother if there was end result and no benefit in it, its only easy to justify doing something for something I want. But if you're talking justification in some intrinsic morale good, then no, as ultimately either every act counts or none of them do.