"Or maybe it's not really a "hierarchy of importance.""

Religious rights can be overridden by the notwithstanding clause.  
Democratic rights cannot.

Clearly then, the two types of rights are afforded a different status, even if both are subject to reasonable limits.

ps:
I didn't say separation of church and state is in Canada's constitution,  only that it's a wonderful aspect of Western world, especially when compared to some repressive Middle Eastern regimes.  Don't you agree?