You described well why humankind has united. For the first time in human history there was an outside gaze and they did not want to look petty in the eyes of the Vulcans. Although neither species wanted this quality of their relationship there was a paternal element to it. The Vulcans have been the father who overlooked the progress of their son and the son had to rebel to get out in space.
But we don't know what happened in the ninety years between first contact and the launch of the first warp 5 vessel so the unification (being the old lefty that I am I was about to write unionization) did not happen overnight and might have very well taken decades. It could have been a very bumpy ride with some wars and as you pointed out once warp-capable ships were mass-produced a faction with a totally different philosophy might have left Earth. But I have my doubts that there are still such major differences once warp ships become affordable. Leaving your homeworld is also a pretty big step.
I think that the cargo crews in ENT were more realistic. They did not want to get out of United Earth but they weren't particularly nice, exploration-hungry guys happy to meet aliens either, they were simply people on the frontier where life is rough.
About the Maquis, you indicated that there is a trade-off between centralization and representation which we also experience at the moment in Europe and which is even a frequent political issue in the US. This would clearly have also been an issue during the unification of Earth.
But isn't the crucial question is in what way fictional history provides dramatic material? Trek has mostly used fictional history as background. Let's take eugenics, besides knowing that one happened earlier we can't clearly tell the difference between the Eugenics War(s) and WWIII but it serves as a fuzzy background for characters like Khan, Green, Bashir and Paxton. And isn't that how events from a century or two ago influence us in the real world? History, just like personal memory, has usually more in common with a spectre than with hard facts.
Talking about spectres, I am no stupid Marxist but wouldn't this be a great propaganda line: "A spectre is haunting humankind — the spectre of a United Earth."