^But that's not the ending. You're distorting it by leaving out the final line of the scene. Nadet gets the last word by urging the Novans to listen -- and of course there were nuances in performance that aren't in the transcript. The implication is that Nadet's view -- that the Novans should trust the NX-01 crew, accept the truth about their origins, and allow themselves to be resettled -- is the one that ultimately wins out. Hell, the characters in the final scene certainly wouldn't be so happy if they'd just left the Novans there to die.
And I didn't interpret T'Pol's comments to be advocating absolute isolation. She just meant that Archer should respect that the new culture and identity they've developed is something they have a right to keep, that he's making a mistake by assuming they should just be taken back to Earth and reassimilated. The solution is to move them to a safer part of Terra Nova where they can prosper and continue to develop their culture, but that certainly doesn't require total isolation -- it just requires not uprooting them back to Earth.