They could do all of that stuff without your fingerprints, why would they need them now? Do you think that Apple is lying about this scanner and the 5s will collect our fingerprints without your knowledge? To what end?
YES, there are people who no longer trust the government or Apple who is cooperating with the government.
It is not like Apple has not misled us and our government has not just plain lied to us. I am not worried as the government got my prints long ago when I got my concealed to carry permit. I still do not trust them.