Back when I first saw it with my teenaged eyes, I was heavily on the Federation's side - how could I be anything else when the series is centred around (mostly) Starfleet officers?
Over time of course when your views about life and the world are better informed/more cynical, then I tend to sympthise more with the Maquis. The Federation did a truly horrible thing, and it's one of the reasons that makes Voyager a little odd as a series with the crew getting on so well so quickly. How can such betrayal be forgiven so quickly?
The formation of The Maquis is a harrowing wake-up call for Starfleet, and indicates that hostilities with the Cardassians must have been pretty bad to make them resort to such a treaty. We've had some indication of what things were like through O'Brien in particular, but I agree that this episode just comes out of nowhere in DS9's universe. And yes I totally agree that Journey's End on TNG was hapless as the beginning of the Maquis arc.
But very good episodes altogether. The presence of Dukat here is welcomed, as him working with our guys muddies our expectations even further.