I don't see how his action was insubordinate and definitely deserving of punishment, he changed policy/tactics after the Borg were significantly changing what had been agreed to. If Janeway had been in command all the time I imagine she would have at least been very conflicted, if not indignant, about going at least 5 days in the wrong direction, deep into Borg space, she would have had her own trust in the Borg pretty eroded even if it survived and she did agree to do so.
If I remember well, just before Janeway undergoing her operation, she clearly tell (=ordered) her XO to make the (unexpected) alliance she has concluded with Borg work, what meant making some concessions if required, because as well the crew as Borg on board, had everything to gain.
But Chakotay, once in control of Voyager, despite his promise to honour the original agreement, took the decision to end this alliance here and now,, arguing that now he was in command, he had to do what he thinks was best for the crew
-> for the crew ...or for himself, he who was so vocal in his opposition to make any alliance with Borg. I remind that his decision to end any alliance spent with Borg happened before the discovery it was them who have started hostilities with Species 8472. Seven was right when she declared that "
Every individual entitled to their own small opinion. You lack harmony, cohesion, greatness. It will be your undoing.
And don't get me wrong, Chakotay perfectly knew that in acting like this, he countered Janeway's orders when he visited her while she was still in a comatose state.
[Sickbay]
(Chakotay briefs his comatose Captain.)
CHAKOTAY: 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.
=> I disobeyed your orders, Captain, but I hope that as your friend, you'll understand my decision.
Or at the end,
[Da Vinci's Workshop - night]
(Janeway is at a desk, writing with quill on parchment.)
CHAKOTAY: Am I interrupting?
JANEWAY: Not at all. Just finishing up my log.
CHAKOTAY: The old-fashioned way.
JANEWAY: I wanted to get as far away from bioimplants and fluidic space. And this feels more human somehow.
CHAKOTAY: I hate to spoil the mood, but you might want to look at this Engineering report. It'll take at least two weeks to remove the Borg technology from our systems. B'Elanna did note that the power couplings on deck eight work better with the Borg improvements.
JANEWAY: Leave them. How is our passenger?
CHAKOTAY: The Doctor says she's stabilising. Her human cells are starting to regenerate.
JANEWAY: I wonder what's left under all that Borg technology. If she can ever become human again.
CHAKOTAY: You plan to keep her on board.
JANEWAY: We pulled the plug. We're responsible for what happens to her now.
CHAKOTAY: She was assimilated at a very young age. The Collective's all she knows. She might not want to stay.
JANEWAY: I think she might. We have something the Borg could never offer. Friendship.
CHAKOTAY: I want you to know that disobeying your orders was one of the most difficult things I've ever had to do.
JANEWAY: I understand. And I respect the decision you made, even though I disagree with it. What's important is that in the end we got through this, together. I don't ever want that to change.
CHAKOTAY: Agreed.
JANEWAY: Good. Well, I think it's time we get back to our bridge.
CHAKOTAY: No argument there.
(We are given a last lingering look at Seven on a biobed, one small implant blinking.)
And once recovered from her operation, Janeway clearly asked Chakotay to explain his actions
[Sickbay]
(Janeway is up and back in uniform.)
CHAKOTAY: Captain?
JANEWAY: The Doctor brought me up to speed, but he couldn't tell me what I really wanted to know. Why?
CHAKOTAY: The Collective ordered me to reverse course, travel forty light years back the way we came. What would you have done?
JANEWAY: I probably would've reversed course. Maintained the alliance as long as possible.
CHAKOTAY: In my mind, the alliance was already over.
JANEWAY: You never trusted me. You never believed this would work. You were just waiting for an opportunity to circumvent my orders.
CHAKOTAY: Trust had nothing to with it. I made a tactical decision.
JANEWAY: And so did I.
CHAKOTAY: They have taking advantage of us from day one.
JANEWAY: We made concessions, so did they.
CHAKOTAY: They lied. The Borg started the war with Species 8472. We've only got one Borg left to worry about. We should try to disable her and get back to the Delta Quadrant. We might be able to duplicate the deflector protocols they used to open a singularity.
JANEWAY: No. I won't be caught tinkering with the deflector when those aliens attack. There's no other way out of this, Chakotay. It's too late for opinions, it's too late for discussion.
It's time to make the call, and I'm making it. We fight the aliens in full cooperation with the Borg.
CHAKOTAY: I was linked to a Collective once, remember? I had a neurotransceiver embedded in my spine. I know who we're dealing with. We've got to get rid of that last Borg and take our chances alone.
JANEWAY: It won't work. This isn't working either. There are two wars going on. The one out there, and the one in here, and we're losing both of them.
CHAKOTAY: It will be your undoing.
JANEWAY: What?
CHAKOTAY: Our conflicted nature. Our individuality. Seven of Nine said that we lack the cohesion of a Collective mind. That one day it would divide us and destroy us. And here we are, proving her point.
JANEWAY: I'll tell you when we lost control of this situation, when we made our mistake. It was the moment we turned away from each other.
We don't have to stop being individuals to get through this, we just have to stop fighting each other.
So, yes, while Chakotay was in command, knowingly disobeyed Janeway's order, only driven by his irrational hatred of Borg*, and for that, he would have deserved to be punished
* (can you imagine that without being threatening towards him or the crew, he has
thrown 2 Borgs in space and wanted to disable Seven, by failing to eject her too ...and he said to have become a man of peace who is against death sentence!) having been , regardless they are adults or kids I bet that if there had been an official Cardassian representative on board (not Seska!), he would have treated him/her with disdain
most of the time.