Although I think this is a politically stupid decision, as it will unfortunately result in driving girls belonging to the most fundamentalistic Muslim families out of public schools into confessional schools or even home, I'm quite sure religious discrimination is not intended at all.
There are basically two approaches at State secularism (or laicity): the French one (which I wholeheartedly favour, even though -- or because -- it implies a measure of utopy) is strictly individualistic. It means all individuals are subject to the secular law, regardless of their religion (or absence of religion), so that religion is a private matter and public space has to be maintained reasonably religion-free. The other (American?) approach is communitarism, which implies the State may have religious groups as interlocutors or partners. In the latter one the door is wide open to lobbyism (we don't even have a French word for that, although we have the reality) and that individuals are utterly left to religious mind and life control. Although the present French position may be seen as rearguard and already lost fight, it still may be valued for what it stands for.