The problem with the Maquis was that the source of their conflict, the DMZ, was now 75 years away. The Maquis were the enemies of Cardassia, not the Federation, and whatever negative feelings they had for the Feds wasn't going to blind them to the fact that these were the only familiar folks around for decades. It wouldn't have been productive for the two crews to be that combative to one another the whole way through.
And even if they were, the tensions would've died down after 1-2 years. If they kept it up after that, then they had to have serious mental issues and they'd likely never get home.
What the show needed was another plot to drive the stories beyond "Going home" which could never be accomplished because...the show would be over.
Voyager lacking an actual plot beyond "lost ship" is one of the core problems. And "Lost Ship" isn't a sustainable premise.
I do agree that the tensions would die down after a couple of years, but imagine the stories you could get out of that 2 year period.
I'd say after things become more comfortable, it's the ideal time to pull a "Year Of Hell" scenario. Have a prolonged, shocking tragedy that Voyager barely survives. Have the ship be pushed to it's limits and many valuable crewmembers perish. The surviving crew would come out of this a solidified unit, regardless of where their original loyalties were.
Then you have fresh drama with Voyager needing to find assistance to get back on the road, possibly taking on exhiled alien outcasts to fill out the crew, which may lead to a clash of cultures etc. It is always going to be difficult to introduce new supporting players to Voyager, recurring enemies will never be given the time they need, so something like this might keep it fresh.