I fully support the complete separation of religion and state, I'd be much happier if non-faith schools here were truly secular rather than having watered down something, as at the moment. Also as Pupuce mentioned there is a whole debate about the idea that you are French before anything else going on, added to all the Nort Africa/France history.
As for the refusing to do P.E., that's quite common here. I did some work for the Welsh sports council and spent time at a high school in cardiff whener about 85% of pupils are Asian and the majority of those are Muslim. Although the school had separate P.E. and swimming lessons, allowed the girls to wear leggings and l,ong sleeve tops to swim in and so on, a majority of girls were not allowed to take part in games lessons. Quite frustrating for the staff and caused a lot of resentment between those (non-muslim) girls who had to endure games and those that didn't. Similarly there were many girls in school who wore bourkas (think Afghan womwn under the taliban)or disappeared when they turned 14 and came back married and then got pregnant.