I have considered putting out a version of the mod with all the unique religion aspects removed. I considered it anticipating that people could be put off or offended by the choices I made in characterizing the different religions, choices that were admittedly biased not only inevitably by my own views, but also by game-related balance issues and particular historical contexts for the developments of religions (Christianity and Islam both come off as militant because I wanted to simulate a militant period of religiosity mirroring our own Middle Ages/Early Modern period, not because I think those religions are somehow intrinsically aggressive).
Giving different religions 'attributes' is always going to be a sensitive area, and I can see why the game designers steered clear of the issue and made them all the same. However, this makes religion ahistorically bland and undynamic, so as long as it's done carefully, religious differences are the way to go (and you've approached the problem with a lot more thought and sensitivity than some other modders have done).
Ideally (and this is something I've hoped for for a while) the religions in civ wouldn't have to be given hard-coded names, and could instead be created dynamically, in the same way that dynamic-civ-names works. E.g. if the Indians found a polytheistic religion, it gets called 'Indian Polytheism' as opposed to 'Hinduism'. So no more worrying about offending Christianity or Islam, because in game they would be 'Roman Monotheism' and 'Arabian Monotheism' respectively. So your game of civ could quite happily see bloody, agressive crusades in the name of 'Viking Monotheism', or whatever, and no-one could take it personally. Problem solved. Unfortunately, I suspect that this would be impossible to mod currently.
Incidentally, I find it strange that the developers avoided giving traits to religions, but were quite happy to stereotype entire races with in-built differences. Personally I find this to be far less justifiable (although Civ 4 isn't as bad as Civ 3, where the civ differences were down as racial traits rather than leadership attributes). Most historians will tell you that differences between civilizations are largely down to economic/geopolitical factors, nothing to do with race at all. E.g. an unforgiving landscape like Mongolia lends itself to nomadic lifestyles and the use of horse archers, wheras the rich, productive farmland of ancient Italy lent itself to the use of well-supplied, well-equipped Roman legions.
Anyway, just want to say, nice work with the mod, it's really refreshing to see someone who doesn't think chucking 800 extra units and buildings at the game somehow makes it better, and is in fact more concerned with historical gameplay and balance.