Considered the Prime Directive declares it moral to watch an entire race die in a natural disaster because you don't know the consequences of getting involved... I'd say a bit of overeaction against something like that is small change.
And of course DS9 turned a blind eye to Starfleet regs a lot of the time. That was the whole premise of the show. It's a Bajoran space station on the frontier where the Federation's presence isn't as big. One of the active elements is a renegade group of Federation citizens(always found it funny DS9 made far better use of the Maquis than Voyager where they were around every day), and once the war started, it progressively became a "win at any cost" struggle.
Frankly I wish we saw more of that attitude on Voyager, it made for some good drama. The conflict between Janeway and Chakotay in Scorpion for example was just bittersweet in so many ways as it gave a glimmer of what the show could've been.
DS9 used the Maquis as a focal point in more episodes than VOY, yes. But the Maquis thing totally got overshadowed by the Dominion. It was hot news for a few episodes then they brought it back once in a while for convenience I think. Also...WTF...why DIDN'T Starfleet protect them or try to cooperate with them? Weren't they still considered "Federation citizens"? It seemed as though they were somewhere in between being in the Federation and not. I know Sisko went to the Maquis and tried to help and they refused...but in their minds they had to protect their homes. I think Starfleet could have done...SOMETHING to help them.
And yeah Voyager just didn't deal with the Maquis in the right way. Then again being lost in the middle of nowhere with little hope of returning home was understandably at the forefront of their minds. When something THAT bad happens...it's conceivable to think that past pettiness might lessen a lot. However, it would have been entirely conceivable for the Maquis to put up MORE of a fight against Janeway for destroying the Caretaker's array. We only got one cry from B'Elanna and that's it. And Chakotay just bent over and took it. Like you said, episodes where there was ACTUAL tension between former Maquis and Starfleet seemed more realistic. I honestly did not like when Chakotay and Janeway fought because I ship them as a couple in my fanfiction/fantasy world.

However, I did enjoy the tension in "Scorpion" and a few other episodes where they had a conflict of interest.
I still love when Chakotay punched Dalby in the face. I liked "Learning Curve". They finally showed the Maquis not cooperating!
[YT]http://www.youtube.com/watch?v=zQwQdVyecz4[/YT]