Any company, individual, or government will discourage investigation. Sometimes, because they have something to hide, sometimes, because they want to avoid precedent, and sometimes, just because it's a big fat pain in the butt, and they have the resources to interfere.
I'm not saying that Apple is right or wrong, here; just that this particular thing isn't really something to get all worked up over. The people pushing this, have an agenda (as does Apple, or any corporation). They are framing the matter in terms that will fit their perspective.