Newt may not be overly familiar with the American wizards and witches, however he is all too aware of what they will do to anything that they class as 'dangerous'. He knew that they would want the Obscurial destroyed, as far as they were concerned there was no way to safely control them - therefore they could see no alternative. Newt knows better. He couldn't do anything for the girl in the end but this one, this one he would save. He would find a way.