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?