Eh, I think the Voyager crew would have started to make a lot more moral compromises if they were in Equinox's position, but I don't think they would have gone as far as to murder innocent creatures.
They might, however, have gotten rid of their 'No sharing technology' rule, tossed aside the underdeveloped species noninterference clause, or had a different attitude in cases like Prime Factors or False Profits.
That would have been an awesome storyline where the ship is on the brink of destruction, and Janeway finally caves "Okay, we'll give you replicators if you help us".
Also it would have been great to see the real Maquis philosophical differences. I don't think they should have rebelled and taken over the ship. But, every time the Maquis were differentiated from the Federation they were portrayed as if the 'Maquis way' was behaving like opportunistic thugs. The Maquis were never portrayed as thugs in DS9, the Maquis we meet have the same kind of moral certitude as the Federation with different morals. Chakotay should have been pushing Janeway to say, support rebels against tyranny.
That would have been a great episode. Voyager runs into a semi-reasonable dictatorship. One that's not going around slaughtering people, but are still tyrannically oppressing people. The dictatorship makes a deal with Voyager to cross their space. They then come across colonies of people who are fighting for their freedom against the dictatorship. Prime directive, yadda yadda yadda, can't interfere. The Maquis start secretly sending supplies to the rebels, and some of them even want to stay behind and fight.