"I fear more than that the chemical action which would be set up in my soul by a false homage to a symbol behind which are massed twenty centuries of authority and veneration."

In other words, Stephen's disbelief in God is not complete. It could not be, after he has been through so many years of religious upbringing. He cannot deny the authority gathered over a vast amount of time by Christianity. He has lost faith, but not to the point of no return.