The Overlord wrote:
But really the network and writers should have worked this out in advance, if the writers wanted a Maquis-Star Fleet conflict storyline, but the network didn't want any conflict, they should have agreed to drop the Maquis angle.
I doubt it would've been that simple. It would've been an ongoing process, as the producers developed their show, the network gave notes, and the producers tried to balance those notes with their own goals. Maybe the network execs didn't decide to ask for the Maquis aspects to be toned down until after they'd seen the pilot. That happens all the time -- things get put into pilots that the network decides it doesn't like, so they get abandoned. That's part of what a pilot is for. It's one thing to read about an idea in the abstract, but you often need to see it actually there on the screen before you can get a feel for how well it works. So things often show up in pilots that get discarded afterward. For instance, in the original Battlestar Galactica
pilot in 1978, the character Cassiopeia was a "socialator" -- implicitly a prostitute in a society where that profession was legal and respected, foreshadowing Inara on Firefly
but addressed more indirectly due to censorship of the time. But the network objected, and by the second episode she'd become a nurse. And there are plenty of pilots -- two that come to mind are The Flash
and The Invisible Man
(2000) -- where the heroes have girlfriends who disappear without explanation by the second episode.
You can argue all you want that the Maquis element is more important than those and that they "should" have worked it out in advance -- but the bottom line is, you can't always know. It's not a single discussion that leads to these decisions, it's a whole ongoing, evolving dialogue with both sides pushing for what they want. It's a complicated business, and it's easy to be an armchair quarterback and claim to know what they "should" have done, but if you actually had to do the job yourself, you'd find it wasn't that simple by a long shot.