Chakotay as second officer strongly disagreed with Janeway's command decision even after explaining her reasons. That happens in real life.
He wasn't willing to stage a muntiny over it and probably didn't think he could anyway. But when an oppurtunity arose to circumvent her without attemping a very risky coup and burning all his bridges he seized the chance and took what he felt was the far better course of action.
Sorry but,
1) Chakotay didn't react/act with with wisdom here but led by an old visceral fear come from his young years. Result: it failed & worst, he took the risk of alienating 2 enemies (Species 8472 & Borg, which are,with no doubts, the most dangerous of species met in DQ), among which the last ones which have collaborated rather faily - until his decision to end the agreement -,.because they had so much to gain of the past temporary alliance themselves). instead of one, while Janeway has chosen to share knowledge and experience with Borg to fight Species 8472. And even if that tactical decision (to make alliance with a dangerous enemy to get rid of another enemy as much - if not more - dangerous, just to rebalance the strengths*) was maybe risked and certainly unusual, but it worked and, at the end, it's thanks to Seven's iintervention that Voyager managed to get out of the trap, without too much damage at the human level.
* Besides, wasn't Chakotay himself, who has at first, adviced Janeway to act like this, in engaging alliances with different Kazon clans/tribes to thwart Cullean?!)
-> alas, it failed and at the end, Janeway "chastized" ... and we got a speech on Starfleet principles, remember?
2) what bothers me her is that, while Chakotay said to have made his decision, even if he knew that in acting like this, he deliberately circumvented Janeway's orders but at the end of the episode, when the tangible tension between both commanding officers eventually dissipated, he went to
apologize to his Capitain, not to have dissolve the alliance spent but to have disobeyed : 'I want you to know that disobeying your orders was one of the most difficult things I've ever had to do").
I mean, wasn't it a little bit hypocritical step from his part knowing that, when he visited her in Sickbay, while she was in the coma - and so, unable to stop him -, he informed her to have made his decision as the higher senio officer in command... and friend, as if he looked for her forgiveness : "Well, I've made my decision. If it were only a matter of going against the orders of my superior officer. You're more than just my Captain. You're my friend. I hope you'll understand").
Come on, while Janeway was out and that he found himself in command of the vessel, he took a decision. No matter that it was a good or a bad one. He made a choice. It was his. So, that he assumes! Why to look for fogiveness, while the other person was unconscious and so, clearly unable to oppose any resistance and/or later, when he went see her to tell her how sorry he was to have acted like he has done? Have you already seen Janeway apologizing for décisions she has made while she was in command? Nope. That she regretted not having been able to act differently knowing what had been the price to pay in human lives (and we know to what extent the well-being of her crew means a lot for her), yes but NEVER, she would have had the idea to go to give forgiveness and/or apologizes with whoever. She assumed, as capitain, all her successes and her failures. She wasn't perfect as an individual but, as a leader, she was a good one for whom the expressions like "take a chance" or "leap in the dark" were foreign to her vocabulary. During 7 years in DQ, she just acted in the interest of his men..., what did not prevent her from making errors.
Plus, you say that "when an oppurtunity arose to circumvent her without attemping a very risky coup and burning all his bridges". Really? We are many to think that this episode was the second one of a long series, where Janeway did not see anymore Chakotay as a man of a total confidence. Her trust in him dissipated in spite of her numerous declarations of friendship and confidence -> did she do that with Tuvok? NOPE. She made him one and only passionate declaration about what their so long friendly relationship represented to her. And even there, she always knew that she could rely on him.
It seems to me that both commanding officers of a vessel have to work together and for that, they have to share a mutual trust, especially in the situation in which Voyager and her crew were, not acting one against the other, like they will often do afterwards. When she says that she respects the decision, she does it considering that Chakotay took it as the only valid commanding officier in command at the relevant time, but she adds quickly after that, still as commanding officer herself, she still disagrees with the decision taken, what means that IF she had been fit to act/react at the relevant time, she would have strongly opposed to him, even if it meant suspending him).
There is a time for the emotions and another one for a conscient leadership and during this lapse of time, it is sometimes necessary to disregard our own feelings because it darkened the judgement.
Anyway, for me - and as we would say here, Chakotay "a joué petits bras" (he ducked underneaths here) and plus, he was wrong AGAIN. My, I know that in books, he was promoted as the Capitain of Voyager but in the series, if Janeway hadn't been fit anymore to command Voyager, the vessel would have been destroyed en route and/or there would have been more human losses (and I don't speak to you about numerous mutinies led by Tuvok and/or Tom/Harry which would have taken place) under his command so much his command decisions were risky during their long journey of 7 years!
