I think you are nearly on to it Denny. Conscience is the human functions that many think makes man in the image of our creator. However, the morality code that the conscience uses in the referee process must be learned. That comes from the religion(s) dominate in the society of the child. The child does not acquire the code directly from religion but indirectly via his society where the code is passed from generation to generation via religion. We generally do not have difficulties with other societies with different religions as the morality code is close in most religions. Jews, Hindus, Buddhist, Christians Taoist and more, all quite compatible, perhaps even complementary for those that gather from more than one. So the atheist did not invent a secular morality, he just uses the one around him and I think, the Pope was speaking to this reality. No reason to reject the atheist at the pearly gate, if he has been walking the walk, following the conscience.
That conscience is not loaded the same though when the moral code is acquired from the teachings of Mohammad. Followers of all of the above listed religions including the atheist that only indirectly acquired the code, are lessor humans in the consciousness loaded with the code acquired from Mohammad. No other religion has the exclusionary prejudice like the concept of Infidel, to be abuse, used, sold, and ransomed, even cut his head off, no one will care.
