That is based on an assumption, we don't know what transpired between destroying the Array and the scene where we saw them all in uniform. I can and have made the case that becoming Starfleet was Chakotay's idea. For all we know they all voted to become Starfleet. You would like to believe this, but that doesn't make it true.
In fact you are also assuming that basic Federation and Maquis values are different. Based of what we have seen they don't appear much different.
It's not invalid, especially when you consider an episode like Learning Curve where the inept Maquis are put through demeaning training to "shape them up" and basically get them to conform to Starfleet standards.
Not knowing what happens "between scenes" is a flimsy argument with no substance. Not to mention circular at best. For example, on the opposite side of that extreme coin Janeway could have had her security people put phasers to their heads and ordered them to join or die. Making up stuff between scenes is the realms of fanfiction pretty much.
As established in DS9, these were freedom fighters willing to do anything to defend their homes and win freedom from the Cardassians. The Federation turned a blind eye to their problems at best to actively aiding their enemies at worst. And we're supposed to think that they'd want to join a Starfleet crew without a hitch? Not likely.
As for sharing the same values? Similar perhaps, but as I said it was Federation values that led to them turning a blind eye to the Cardassians oppressing them. Couple this with them being a fringe group, doing what it takes to survive, then you have Janeway telling them that she's willing to sacrifice their lives over a replicator because of the Prime Directive, and you don't think they'd be resentful over that? Heck Hogan the all around "good Maquis" looked like he was one step away from maiming Janeway in that scene alone.