Even though Harker wasn't raised to any religion, he was familiar with several Bible stories from his mother, who was raised by a devout Catholic family down in New Orleans. Now how devoted Josephine Jones was can't really be determined, and not really all that important.
Harker always thought her to be more of an agnostic, though he did occasionally see her pray during the roughest periods of their lives while she was still alive. That was mostly the reason why he didn't question Father Gerard's behavior when he was pretending to be her. When Chloe was born, he also did notice her carrying a rosary in hand more often.
When he was younger, he didn't think much about these things. But now that things had evolved this way, he felt he shouldn't run from the past anymore.
His mother knew something. She could feel it, as the years approaching her death from childbirth came.
But what? What was she so scared about?