The United States is still living down the shame of centuries of slavery and of the internment of Japanese-Americans in WWII. So there's plenty of historical reason why many American citizens and politicians would object to the idea of the permanent internment of any population. Maybe today it's easier to believe that we'd tolerate such a violation of civil rights because we've allowed our regard for civil rights to become so badly eroded in the years after 9/11. But we're talking about the 1990s, when those principles had not yet been undermined to the same extent.
Besides, there may have been pressure from groups other than civil libertarians. Business leaders might've wanted the Newcomers freed from quarantine so that they could be exploited as cheap labor. Also, the government would surely have been interested in their technology. Those Newcomers (mostly Overseers) who had some insight into the technology or advanced knowledge of their enslavers may have offered that knowledge in exchange for being freed from quarantine, or the government and corporations may have needed them to be out of quarantine so they could be brought to labs and so forth to teach what they knew.
Plus there's the security concern. Someone else, some more powerful alien race, enslaved the Tenctonese. How do we know they won't find and enslave us? It would've been in our own best interest to get on the Newcomers' good side and gain their cooperation in telling us all they knew about their enslavers.