John, I’m with you on the bum rap that relativity gets on this score. It’s about as rigorous as arguments that say quantum mechanics (or if the speaker is feeling really fancy, Heisenberg’s Uncertainty Principle) tells us that no knowledge is possible.
I think the Pope’s broader argument is that viewing humans as machines tends to lead us naturally to treat others as objects. It is often asserted casually that contemporary biology can show this premise to be true. As I see it, Pope Benedict is pointing out both the implications of the premise and the fact that it has not been established.