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I'm not French, but that's my impression what France wants to be: a secular society. There is religious freedom, but you are not supposed to impose your religion on others. The French want citizens who take their civic duties seriously who vote and participate in the political process. So if you apply to become a citizen they want to know if you are willing to contribute, if you are willing to stand for the ideals of their republic.
I think looking at it from this perspective it becomes clear why they wouldn't want this woman to become a citizen. Citizenship would be an advantage for her, but it would be a burden for the rest of society.