Janeway took advice from her male confidants but she was more than capable of making her own decisions and going against her advisors if she felt the situation warranted it.
The problem is not to see Janeway surrounded by male representatives but rather the fact that STV's producers felt the need to show her often seeking advices of her 2 confidantes before making a decisions. Did you see Picard, Sisko or even Archer doing the same thing?! Nope.
As for Chakotay-I don't think recall him being critical of Janeway that much-Equinox, Scorpion, and maybe a few other times. He may have not always liked her orders but he followed them most of the time.
Uh?! Sorry but If there has been cases of direct confrontation between Janeway & Chakotay, it was in Scorpion & Equinox :
- in Scorpion, Chakotay set, from the beginning, against any collaboration with Borg and took advantage of the first occasion where Janeway had his back turned, (in fact, she was seriously injured and had to have surgery quickly), to turn his back on this commitment she has taken. Action which earned him an serious admonition (and contrary to what many of you think, she didn't relieve him from office at this time, prefering to use him to connect with Seven via the joint mind - Unity 3x17 - under the Doctor's care!)
- in Equinox, while both commanding officers violently opposed on the way to act with respect to Ransom and his crew after Seven's removal & the theft of Voyager's equipment, Janeway decided to use some old technique of psychological torture to make him talk, asking her XO not to intervene, but Chakotay disagreeing with this approach, didn't hesitate to commit an act of insubordination in freeing the Equinox's Lt . For this intervention, she relieved him and I think that it was the only occasion she did it.
-> did she cross the line, maybe but in her defense, we know how protective of her crew and vessel she is. Here, she felt in war against Ransom and his crew...
About Lessing, I'm pretty sure that she would have stopped at the very last minute, as she tried to save Ransom in spite of all he has done and in spite of her given word to deliver the Equinox's Captain to aliens (the latter prefered to commit suicide in making explose his vessel). However, I'm not so sure that Picard, Sisko and Archer would have act like Janeway.. I mean that they would not have hesitated to deliver Lessing and Ransom if they had felt that they were a necessary sacrifice to save the crew and their vessel.