Maybe the Maquis were the most boring terrorists ever because of a refusal to portray them as terrorists.
It's absolutely true the Maquis rebellion has no application in the DQ, it's absolutely rational for them to work with the Starfleet crew. But, I would think the 'Stopping at every nebula to do scientific research' and the general self sacrifice on principle would piss them off more than it did.
If it was UPN who prevented them from having conflict between Maquis and Starfleet, maybe I've been too hard on Berman all this years, and I really should be blaming UPN. It sounds like all of Voyager's failures were due to the false assumption that not taking risks out of fear that you might rub people the wrong way would lead to long term higher ratings.