I mean, that logic was only ever applied by the Vulcans as a personal choice/sacrifice, not something to be enforced by the barrel of a… er… phaser.
Spock sacrificed himself, it wasn’t done forcibly against his will. Kirk didn’t order the execution of one man so that others could live.
I don’t think we should take a slogan as an absolute moral lesson, you can justify all kinds of evil with it.
E.g. your organs could save dozens of lives. Would it be right to pin you down, kill you, and remove them, so that others can live? Surely one life lost is a worthy price to pay? The needs of the many outweigh the needs of the few, after all.
Ethics are a lot more complex than a catchy slogan.