ROB, if Chaza”l identified the reason for a punishment, we don’t question it. You’re practically bringing them down to your level when you say that if you don’t know the reason for punishments, then they must not either. I don’t see how that that’s not kofer b’divrei Chaza”l.
I happen to subscribe to the view that Chaza”l didn’t err in science; as the gemara itself says about this inyan, ??? ?’ ??????.
I just don’t think you can call it kefirah to hold otherwise if the Pachad Yitzchad (Lapronte) did so, although we don’t pasken like him.