Just one word: Equinox.
"Captain Ransom has violated and dishonored the most fundamental principles of Starfleet, so he has to be stopped
at all costs... even if it means that we have to torture or murder one of his crewmembers!!!"
It were episodes like this which made me wish that Chakotay had been in command sometimes. And something like this never occurred to me while watching the other Trek series... I've never asked myself "why can't Riker/Kira be the Captain/Commander???".
Yes, that poor Noah Lessing in
Equinox! He and his crewmates were committing genocide and had left the Voyager crew to die at the hands of the aliens they were killing. Gee, can't a murderer catch a break?
Yes, Janeway got royally pissed in that episode but in my opinion she had every right to be. I compare her behavior in this episode to Kirk's in
Obsession where both captains allowed their anger and desire for revenge to get the better of them
for a while. Both Kirk and Janeway eventually snapped back though mainly because they had people around them who wouldn't let them dive completely off the deep end.
That's not the point... it's not so much about morality, it's more about
consistency.
In "Equinox, Part 1" there's a confrontation between Janeway and Ransom in which the latter tries to justify his actions by explanining that half of his crew had been killed and that the remaining half hadn't eaten in over a week when they started to kill the aliens. However, Janeway insists that a Starfleet officer has to adhere to Starfleet regulations no matter the circumstances and that there are no exceptions to this rule. Period.
In "Equinox, Part 2" Janeway suddenly starts to break Starfleet regulations herself by seemingly instituting a "Two wrongs make a right" policy. So, a Starfleet officer has to adhere to Starfleet regulations no matter the circumstances... except when a fellow Starfleet captain has pissed you off by killing innocent aliens and attacking your ship.
This at least made Janeway look like a hypocrite.