Ironically, my issue was mainly with the implications of this line. I was under the impression that T'Pol was suggesting that their culture and existence needed to be protected even though it's (mostly) forgotten its Earth-based roots.
ARCHER: We have to convince them that returning to Earth is the right thing. We can't take them by force.
T'POL: Are you certain it is the right thing?
ARCHER: What are you talking about?
T'POL: When you get them back to Earth, what will you do? Send them to school, teach them to read and write, wear human clothing, eat human food, teach them to live on the surface, enjoy the sunshine?
ARCHER: You're damn straight. They're human beings. It's their birthright. It might take a little while, but they'll adapt. It's a hell of a lot better than dying down in those tunnels.
T'POL: They've lived in those tunnels for three generations. You can't just pluck them up and bring them to a strange world and hope they'll learn to conform. You'd be destroying their identity, destroying the Novan culture.
ARCHER: Archer to Tucker.
I was more under the issue the objection was not resettlement but exposure to outside influences.
Also, the episode implied (for me, that Starfleet wasn't coming back)
ARCHER: Your planet has three large islands to the south. We call them continents. The climate is nearly identical to your overside. We don't know how similar the underside is, but my people are working on that now. The important thing is, the poison rain never fell there. You'd be safe. Your children would be safe. You could even spend time on the overside if you wanted to.
JAMIN: If our tunnels are infected you wouldn't want them so badly.
TRAVIS: We don't. We only want to help you, make you healthy.
ARCHER: Was that photograph of Vera Fuller and her daughter shale? Do you really believe we created it to trick you? You're human. So am I. Humans help each other.
JAMIN: When we track back to the underside, we'll return your crewman only if you promise to leave.
The ending isn't too optimistic either.
JAMIN: They promised to leave. Let them go. We'll be fine here.
NADET: We're not fine. None of us is fine. We're rotting, all of us.
JAMIN: They've promised to leave.