In this week's instalment of the CW show, Blair (Leighton Meester) began to turn to religion following her car crash with Chuck (Ed Westwick).
Safran has now defended the storyline and explained that religion has always "been a part of Blair's life".
"We really did believe, especially in light of what has happened to Blair after the accident, that she feels even more strongly about this connection and this pull," he told TV Line.
"It's something that we're not shying away from. It's something that we will delve into in future episodes."
Safran acknowledged that the religion storyline is "definitely a different thing" for Gossip Girl to explore but claimed that the writers believe "this is where Blair is right now".
"Belief is a very personal thing, and it's also very monumental," he said. "We're not treating it lightly."
Safran recently revealed that Blair will find herself in a "love square" in future episodes and hinted at developments in her relationship with Dan.
Gossip Girl airs on Mondays at 8/7c on The CW.