I am here to explain this once again. Neelix and Tuvok were dead. They died in a transporter accident. They died painlessly and unaware of their fate. Tuvix was not dead. Begged not to be killed. And was painfully aware of the fate they were forced to suffer.
It does not matter if you have a magic wand that can magic two people back for the cost of one other, she chose to kill someone, who was begging to her face to be spared. It is as simple as that. What other innocent people would you choose to kill in order to bring back others you deem more valuable? The closest parallel I can think of in the real world would be if someone bundled you off the street and explained that they were going to remove your heart to give it to Joe Biden as you are the best blood and tissue match, and because he is more important than you. You won’t survive this procedure but let’s be honest, Joe Biden is way more useful to the establishment than you, whoever you are.
The episode is great and I would never ask for it to be changed, it added a lot of depth to Janeway as a character, but it was also straight up murder.