9. Stranding Voyager In The Delta Quadrant (Caretaker)
Here is the big one, second only to the execution of a being, in the list of Janeway's most questionable acts. On arriving, unwillingly, in the Delta Quadrant, Voyager finds that the Ocampa are threatened by the Kazon. The actions of the Caretaker, a being of immense power, have drained much of the Ocampa's individuality and resilience from them, leading to their inability to fight the Kazon.
More than that, with the Caretaker now dead, his array contained enough technology to make the Kazon a major threat to the Delta Quadrant. However, it also contained the technology to send Voyager back to the Alpha Quadrant. Janeway makes her choice and fires two tri-cobalt devices at the array, destroying it before the Kazon can get their hands on it.
There are deeply mixed feelings about Janeway's call. While nearly everyone can understand why it was necessary, it does strang the crew 75 years (or so they thought) from home. It's enough for former Maquis like Seska and Jonas to seek their own alliances, away from the ship. It leads to quite a number of crew deaths, and this is a call that would sit on Janeway's shoulders for years to come.