I don't think people are that different wherever they are. I think there would be very strong resistance to integration of an alien species unless there was a clear benefit for humanity and even then it would be a big ask for most people. A more likely scenario would be to put them in concentration camps and hope that someone else will deal with it. Either that or put them in self-governing reservations in the back end of nowhere.
However Alien Nation took place in a liberal democracy and while some may have decided to push them into the seas, maybe a reason why they were settled on the coast was to make a final solution easier if it came to that, others would push for full freedom. And a judge, not a policeman/soldier would have the ultimate decision making power over freedom or concentration camp.
Would have it been worth a full civil war? In the show no, however the former white supremacist linked up with other to form a purist group which is stronger then the present day or 1990s Aryan Nation and KKK alliance.