I haven't watched the first episodes of VOY for a while but my understanding was that Voyager was a science ship.
Voyager was stranded in the Delta Quadrant while attempting to recover an under-cover agent who had infiltrated the Maquis.
Which would, IMO, be a rather unseemly mission for a science vessel in any organization but Starfleet.
And the Marquis were against the Federation because they were on lots of exploration missions?
The Maquis were against the Federation because the Federation couldn't muster the requisite military power to force the Cardassians to give up their claims on several disputed colony worlds and let themselves get roped into a bad peace deal that left the Maquis colonies twisting in the breeze.
So, basically, yes.