"Those crucifixes are still direct endorsements of a specific religion by public bodies. That's why they were originally there."

Why something was originally there doesn't necessarily reflect why is it still there. Few women who get married wearing white wedding dresses today do so as an affirmation of their virginity, for example.

Today they serve as a reminder of a cultural heritage, i.e. "Je me souviens", the province's motto. Just as the fleur-de-lys on the flag and on the walls of the National Assembly isn't an expression of allegiance to the King of France, as it originally was, just to the language and culture inherited from that time.

They are not an expression of an active, personal faith, the way choosing to wear particularly extreme religious clothing is.