Oh, and untold is France's fight against various other sects, from Scientology to Raëlians, with similar motivations.
Salafists are not the only ones being fought against... Un roi sans divertissement est un homme plein de misères
I think the reason the nationality was denied in this particular case is that there is a strong opposition between personal values of the woman and national values as assumed by the court.
Voting rights: her religion denies vote for women, so why ask for a voting right? Civil rights: the law garantees a right for this woman to free speech, equal rights with her husband, authority on her kids, right to work, drive and dress as a man, all of them being in contradiction with her religion, so why ask for these? What is nationality apart from that? If you refuse most of the country assumed values, why ask for the nationality? She doesn't even have the worry of asking for new visas, because as a mother of french kids, it is automatically delivered (and valid for ten years, the same as the national identity card).
From the information gathered in the press, I really fail to understand the reasons that led her to asking the nationality. If you come across some more, please let us know. A free fox in a free henhouse!