At the end of the Star Trek: Voyager pilot "Caretaker", Janeway informs everyone that she and Chakotay (leader of the Maquis crew) have agreed to integrate as a wholly Starfleet crew.
Both crews are going to have to work together if we're to survive. That's why Commander Chakotay and I have agreed that this should be one crew. A Starfleet crew. And as the only Starfleet vessel assigned to the Delta Quadrant, we'll continue to follow our directive to seek out new worlds and explore space.
I get that Chakotay would agree with Janeway that one crew working together increases their chances of survival. But what I don't get is why Chakotay is willing to do so as "a Starfleet crew" and all that entails (most notably, wearing Starfleet uniforms and strictly adhering to the Prime Directive). Very few of the Maquis are Starfleet graduates, and as we see in the next episode, two of the Maquis tell Chakotay they're willing to support a mutiny in order to bring about a Maquis-style of leadership.
Why does Chakotay agree to a full Starfleet-style of leadership instead of some sort of hybrid crew that uses aspects of both Maquis and Starfleet protocol as they see fit? That would seem like something that would reduce the amount of tension from the Maquis, and would mean that Chakotay wouldn't be bound to enforce Starfleet command decisions if Janeway were killed and he became the senior officer.