Anyone who's hired as captain, or anyone who's in a position of authority for that matter, must make controversial decisions, that's why they're appointed to be captain, it's their job to make a decision whether subordinates like it or not. There will always be disent and disagreement over decisions, but it's not the role of a captain to please everybody.
That is a gross misinterpretation. A captain does make the final decisions and the subordinates need to follow them, yes. But that's not carte blanche to make unlawful and morally questionable decisions.
Besides, what would Janeway have done had the procedure gone wrong and Tuvix, Tuvok and Neelix died all at the same time?
You don't "know"
that the decision is or is not lawful. Right now as the laws are written in the US, the legal action would be to separate the two, because it is illegal to use any part of a human's body, even after death with out express permission. As far as morality goes, that is a personal decision, my morality may not be yours but it is just as valid as yours. You cannot legislate morality, that's why prohibition didn't work. That's why anti-abortion laws will not work. You can view anything by your own set of moral parameters, but you have no right to impose those parameters on anyone else.
Janeway was in charge, she made a decision and I don't notice Tuvok or Neelix wanting to be reassembles as Tuvix after they were separated.
You can think what ever you want, but you cannot impose your idea of morality on anyone else. If you are captain someday you can make the decision to keep Tuvix, but then you might get sued by Tuvok's family. But what ever you do, there will be those that believe you acted in an immoral and criminal action.
Finally there could be no other outcome for that episode, the regulars had contracts and the guest star didn't. Think about this, do you really believe that the producers wanted to trash their main character, or did the want to show her making hard decisions. I don't believe anyone in charge actually thought that they were showing the Captain of Voyager as an immoral criminal.