The Maquis were frontier people who had struggled to establish their colonies, they were a world apart from people like Picard or Janeway who applied haughty principles and ethics to everything. That was the main difference and that was where the compromise was to take place. Voyager shouldn't have been like Enterprise where every challenge ended in some discussion about Federation principles and an executive decision by the captain, it should have been about being more pragmatic. A properly combined Starfleet/Maquis crew wouldn't have just been waiting for Janeway's decision on whether to clandestinely acquire the technology from "Prime Factors" - there would have been a more open discussion taking in pragmatism and principles. Janeway's decision was basically "we can't break their law so we're not taking the technology", but a decision by a crew that had combined Starfleet/Maquis principles would be "We are breaking their law but we aren't hurting anyone, so we believe its acceptable to do this in this situation as it helps us get home". Ethics and pragmatism can co-exist. Unfortunately we got Janeway's executive decision, scolding B'Ellana for even thinking about going near the platforms to just LOOK at them and the crew having to resort to acting behind her back to get the technology. I mean the whole point of Chakotay being first officer was to bring some Maquis into the command structure on Voyager but unfortunately he became a lapdog way too quickly and we never really even saw him talking with the Maquis or asking them what they thought,.
And that brings me to one of the main problems of the Maquis aboard Voyager situation - the lack of secondary characters. The average Maquis or Starfleet officer never really had a voice, we didn't KNOW what the people on the ship were thinking besides the main characters and that's a huge problem. It was a ship of around 140 people 70 years from home but the emotional impact on the crew as a whole was barely even mentioned in passing. They just continued to saunter about the ship in their color-coded Starfleet uniforms acting like it was any other ship.
Voyager needed far more secondary characters to flesh out the situation and let us know what's going on. I came up with a plot for a Voyager episode where two crewmembers see their friend killed on an away mission and decide to resign their commision and live on Voyager as civilians in order to avoid the danger of a mission they never signed up for.
I don't think that's too far off what some crewmembers could have potentially felt, not everyone is going to be all "let's get going back to earth and we're all gonna do our jobs 100% because we're enlightened future humans", I'm sure there would have been a myriad of different attitudes and approaches to the situation but we saw none of that. There just wasn't any depth to that ship. "Star Trek: Voyager" was basically a vehicle for the writers to tell us a lot of entertaining science-fiction stories, it was never really more than that, it never felt real.