I think anyone who claims the Maquis were just defending their homes is forgetting that they also openly attacked both Cardassian and Federation ships and weren't above poisoning planets to get their way.
While you've got the apparently mild-mannered quasi-Starfleet Chakotay, you've also got the more middle-of-the-road Torres and the batshit-crazy Suder. The Maquis were pretty equal opportunity employers, but in the end I think Voyager generally painted them as being far too eager to put on the uniform.
Seriously, what would happen to those individuals who were willing to join and fight with the Maquis because they were defending their homes, but honestly -weren't- cut out to be Starfleet? Don't tell me Tuvok's little boot camp (which merited all of one episode apparently) had a 100% success rate.
I don't necessarily expect to see people openly challenging Janeway's decisions or such, but some acknowledgement that these people do potentially come from radically different backgrounds and don't all want to become part of a quasi-military hierarchy would have been nice.