"The needs of the many outweigh the needs of the few."

By killing Tuvix, she saved two people instead of 1.

Also Tuvix fucking sucked at making coffee. Janeway needed Neelix back.

So 2 things with it, first out of universe in the real world, the actors have contracts that need to be upheld, simply because of that the ending of that episode had to happen that way. It would have been fascinating to get to do a longer exploration of this character but the reality of producing a TV show is that contracts have to be honored, amd just like Tuvix, neither choice is really "the right choice" just different ones. Is serving an interesting narrative more important? Is honoring the real lives and work contracts of the actors more important?

The second, is that the episode clearly does heavily weigh on the decision that needed to be made, sacrifice the existence of 2 of the crew for a new one, or sacrifice the existence of this one for the 2 crew mates, the episode never made any comment which was the right choice, only that the choice had to be made one way or the other. Hell even The EMH explicitly states he will not take Tuvix's life by beginning the separation. The episode makes no mistake, what Janeway is choosing to do is essentially murder, and only asks us whether the murder of 1 is worth saving 2.

At the end of the day this this episode testing the conculsion of Measure of a Man in the no win decision of the Kobayashi Maru and the logic of irradiated warp engine room from Wrath of Khan. I think its a brilliant moral philosophy episode because there is no good decision, there is no right answer, there is no star fleet protocol that can handle tbis and there is no "bounce a particle beam off the main deflector dish" treknobabble to magically solve the problem. Just the decision of who's lives to change.