I think Janeway was put under stresses that most (perhaps all) Starfleet captains had never had to contend with before. That being said, her treatment of Lessing and Chakotay was out of bounds, and it's laughable to me that Chakotay would apologize to her later. Of course, we'd already seen an alternate Janeway be dismissive of challenges to her authority in "Year of Hell", so this wasn't a complete surprise.
This may sound uncharitable, but I'm left wondering whether the writers felt that the only way to establish a "credible" female captain was to make it so that her decisions, no matter how questionable they might have been at the time, always led to a minimum of negative consequences...and whether at any point they realized how that was actually coming across to many fans.
It probably doesn't help for me personally that the last captain we'd spent any significant time with, i.e. Sisko, screwed up on more than one occasion and, if he didn't face external consequences, it always seemed to me that he at least wasn't thrilled with his own actions. I wish Janeway had shown a little more introspection.