It seemed odd to me for two reasons. One, O’Brien is a military man. The military has a chain of command and its instilled in its members that the chain of command shouldn’t be broken for a whole slew of reasons

You missed a piece in this. When O'Brien went in for his dressing down with Sisko, O'Brien wondered out loud why the transporter wasn't shut down and isolated to O'Brien's com badge location when Sisko realized that O'Brien and his com badge weren't in the same place. O'Brien could not have carried out his plan without assistance from Sisko. Sisko gave a blustery non-answer.

O'Brien wasn't a rogue player here. They all held the same values but were constrained by the Prime Directive. The Prime Directive was the rule that they didn't interfere with other cultures. The Prime Directive is a metaphor of people who go into other cultures and change their cultures for the worse, as was blamed on the Christians in the case of some native cultures.

If Sisko knew about and could stop O'Brien in a second but allowed his actions, was Sisko complicit in the crime?

I don't think it's very unrealistic

If Flynn (a military man) committed an illegal action, and Trump knew about it but allowed it anyway, was Trump complicit in the illegal action? Those are some of the questions the US is now asking.

I think those scenarios get played out in a lot of ways.

In DS9, there's a recurring theme of exploring the point at which inaction or blindly following orders becomes immoral in itself. Picard struggled with it and so did Sisko. They both took actions or inactions they felt were more moral than blindly following orders.

[Edit: removed a possible spoiler] I'll just say here that your questions about what happens when military orders aren't followed is explored a lot.

About the hunters, I just saw a post on reddit yesterday about a hunter who was killed when the elephant he killed fell on him. The hunter and anti-hunter discussion turned so vitriolic that the thread had to be shut down due to death threats. It doesn't seem like the hunter question is very settled. There's not much more to explore.

Those are a ton of questions. Those questions are deep as fuck. Yet none of them were adequately addressed let alone resolved. Tosk went free. For them, the hunt continued. For me, I’m sitting here with philosophical blue balls.

I've read that when a piece of fiction stays with you, it's a great piece of fiction. This piece made you think and question. I rarely see that when people watch things. I think that's a great achievement for a piece of fiction.