Janeway didn't torture Lessing. She only intimidated the evil ensign. Noah was perfectly safe because she knew exactly how Chakotay was going to react. It was all a clever ploy. That's what command is. Know how your underlings are going to cope under pressure and and take that into account when planning your caper.
Later Kathy outright lied to those space beasties, there was no way in hell she was going to hand over even the worst Starfleet officers to be eaten by monsters.
Kirk did that all the time and no one cared.
Are women not allowed to lie?
Meanwhile she had to stay in character when threatening Tuvok, because they didn't know if the space monsters chasing them were watching or/and listening through their shields.
You didn't understand that it was all a cunning ruse?
During the Sting in season 2 when they tricked Chakotay into kicking Tom off the ship, they didn't bring Chuckles into the fold, because no bugger trusted his truly awful, awful acting... There was a novel where after sitting though his one man performance of Hamlet, three crewmen took their own lives.
Chakotay couldn't even act that he was an 8472 acting at being himself without breaking character and blowing his undercover mission. That Archer woman Chakotay made out with was able to hide as a Cylon in plain sight for four years! He couldn't Donnie Brasco it for 15 minutes!
Meanwhile his feelings, get really hurt when you admit that he's been used as a cats paw stooge patsy, so it's best not to award him of the full facts post mission where, when and how he's used.
And his instincts for deception are SHIT!
As captain of the Val Jean, he had a Starfleet Security officer, an Obsidian Order officer, and a Section 31 officer working under him in a ship the size of a shoe box!
It's possible that Chakotay might have some sort of faceblindness or aspergers where he is so incapable of reading facial expressions, that anyone can lie to his face guilelessly in complete safety.