OK, I'll start with an example from "Equinox." (I'd better save the subject of Tuvix for Guy Gardener or some one equally eloquent on the subject).
Janeway tortures Crewman Lessing to get intel on Ransom, against whom she has a personal vendetta. She confines Chakotay to his quarters for stopping her and for telling her that torture is wrong. She tells the aliens that if they'll stop attacking Voyager she'll deliver the Equinox to them. When Tuvok points out that will be certain death for the Equinox crew she threatens to confine him to quarters too.
Then I guess you're hatred for Janeway makes you give Captain Sisko a pass for his vendetta against Michael Eddington. He even orders his crew on the Defiant to fire biogenic weapons at the Marquis settlement, making the planet uninhabitable for 50 years. And threatens to do that to every Marquis planet in the TMZ until Eddington is captured.
Why is it Janeway, who's sole vendetta against Ransom is a legitimate one due to his murder of innocent life forms and attacking her ship, is scrutinized so much while Captain Sisko's vendetta is purely personal, get's ignored?
"Can't you see what's happening to you? You're going against everything you claim to believe in. And for what? To satisfy a personal vendetta?"
"You betrayed your uniform!"
"And you're betraying yours, right now! The sad part is that you don't even realize it. I feel sorry for you, captain. This obsession with me, look what it's cost you!"
"MAJOR, SHUT THAT THING OFF! COMMANDER WORF, PREPARE TO LAUNCH TORPEDOES!"
- Eddington and Sisko, on Sisko's decision to use biological weapons on a Maquis colony
Sisko also ordered the murder of Verad Dax, not unlike your example of Tuvix. I guess another man's worst captain is another man's hero.