Trying to take over a country that just is defending its integrity in WW III, with emergency laws, citizens pulling together and having its military forces on full alert is bound to end up exceedingly badly (unless it is done by military insiders). Imagine trying to start a rebellion in the US during WW II.
Protestants in 16th and 17th century met a little better fate at the hands of the Bourbons.
Besides, the situation with French Muslims is different on two grounds.
1. I
took a look at the demographics and the long and the short of it is that Muslims in France are about as Muslims as French
de souche are Christian and are increasingly behaving like their non-Muslim counterparts in terms of family structure and fertility rate. One might as well predict a takeover of the United States by Hispanics in
23xx (well, there was, but only of part of the United States and that because most of the rest of North America had been depopulated).
2. Another religious minority that once posed a threat to the integrity of the French state were the Hugeunots. Look at what happened to them. The main difference is that whereas the Huguenots were disproportionately literate and highly-skilled urban tradespeople, French Muslims tend to rank low on the totem pole.
The Muslim minority in France was probably somewhat analogous to blacks in the US: bitter and ghettoised, but with little serious interest in trying to take over society compared to a desire to be accommodated and accepted. In fact, the Twilight war might actually have integrated them much more with France: a shared challenge and as France expanded its reach many French Muslims could actually help their family, friends and compatriots.
In a world where the Cold War continued until the catastrophes of the mid-1990s, I'm not sure that Islamic terrorism or Islamism would really have taken off as a widely-perceived threat. The main ideological conflict would have been between the West and Communism. The main terrorist movements might have been left-wing ones, descendants of the Baader-Meinhof gang or Action Directe or the Red Brigades. In this background, practising Muslims might well have been seen as compatriots, especially in the context of an international crisis worsened drastically by the Soviet Union.
By 2320, France includes a very large Muslim population, in Algeria and elsewhere. The story of the Franco-Algerian association has to be an interesting one, IMO.