Is there a respectful way to accommodate anyone's religion in the dojo? I have had to dress down some fundamentalist Christians for their own issues in the dojo, but I do try. Where do the lines get drawn? The lines certainly got redrawn many times over the last century in Aikido.
As I wrote before, if a female student did not want to train with a man, I would be expected to allow this. I would be against a certain level of rank being attained - 5th kyu training with only women would be okay with me, but not any yudansha rank and certainly not a teaching rank. I would question a black belt given to a small woman from a female only dojo. If a Muslim man only trained with other men, would I see his rank as too watered down? Admittedly, not martially.
Reading the news stories about this (my family is from Halifax if that makes a difference) is I can't help thinking that the young lady in question is too easily outraged.