I believe that Carol Emshwiller was indeed making a point about slavery in all forms; however, I believe this was not her ultimate goal. To me, it seemed that she was attempting to point out the possibility that our society could resort back to human slavery. What would our attitudes be toward the issue? Would you identify with the special needs of a Hoot-like species or would you be a wild human?
In some ways, human are already slaves, whether it's to their work, the government, or an organization. I believe that in some ways, the author is making a statement about the different types of humans. Let's face it, there are those who will follow anything the government tells them and then there are others who will investigate for themselves the truth behind the government's "lies." I can see Charley as the ignorant human and his father as an independent thinker.
Just my $0.02.