In Scorpion, Janeway had every reason to believe that Species 8472 would proceed to destroy all life in the galaxy after finishing with the Borg. She had no reason to believe until later that peaceful contact could have been made to explain to them that they are not aggressors just because other organic beings are.
The decision in Tuvix is very debatable. I don't buy the argument that 'Two people are more important than one'. As others have pointed out, this argument makes it ethically permissible to kidnap people off the street and distribute their organs, or intentionally infect people with diseases in order to test your cure. The argument that Tuvix was not a genuine individual due to the way he was created, and they never really stopped being two people carries a little more weight, but that's a huge philosophical debate. And I respected it more in Similitude when Archer came out and admitted his preference for Trip over Sim was selfish. If you have to choose between one life and several, you choose several, but that does not apply here because if Tuvix was a new separate individual, Tom and Neelix were already dead.
To the 'organ' hypotheticals. If somebody stole my organ and gave it to somebody else. If that somebody else was complicit and aware I would steal it back even if it meant killing them, if that somebody else was not I would not, or if I did I would admit I was being completely unmorally selfish instead of making an ethical stand.
I would agree Picard's most ethically questionable action was not using the program against the Borg. A moral stand would have been to defend Hugh's individuality, not send him right back to the Borg.
Sisko had a lot of interesting ethical choices. In The Pale Moonlight was not two people versus one, it was a billion people versus one. The line is somewhere, and it's well short of a billion. I might go for the Eddington thing and poisoning the Maquis planet.
For Janeway it's hard to pick one. Her logic tended to swing arbitrarily between principled and selfish but they never talked about it that way.