This is tricky subject, op, because, culturally and historically, the way women have been treated in a culture, religion or region has changed over time, and women have, even then, been treated differently within a particular context according to economic or social status. We also have to step away from our modern perspectives, and view how religion and culture impacts and has impacted upon different types of women and what is/was seen as more beneficial.
For example, early Christianity was a boon to women from wealthy Roman families because the early concepts of the religion freed them from the rigid paterfamilias system. When it comes to the medieval period, convents allowed women to escape arranged marriages; many also provided an atmosphere where women could read, learn and write. So there have been periods in history where Christianity has meant emancipation and freedom for women. In short, it has been a refuge from patriarchy.
Again, Christianity is also a religion with a highly female divine element. Christianity in Italy and a lot of South America is basically Marianism (the Cult of the Virgin Mary). Jesus and God are pretty much shoved to one side in favour of the Divine Mother, which, of course, is problematic in one sense (godly women = mothers; bad women = whores), but also beneficial in another (the mother must be adored for she is nearest God). In the latter sense, the Virgin Mary has been a very powerful icon for women who are mothers (which, in history, would have been the majority of women over the age of 18); she can be invoked in a political, social and cultural sense to allow women to gain some traction within a patriarchal structure.
Again, I think it is important to recognise that no social structure can continually abuse or repress women at an exceptionally high level for long, and, because of this, few societies have done so. ISIS and Talibanesque attitudes to women within society cannot and do not last for one simple reason: such practices eradicate the population.
Take Afghanistan under the Taliban. Judging by what was already occurring, I suspect the society would not have lasted very long at all, maybe one or two generations. The chronic repression of women through strict purdah led to extraordinarily high rates of rickets in babies and children and other associated developmental and health problems through maternal and infant malnutrition and deficiency. But more importantly, mandatory burqas not only meant that mental health problems amongst Afghani women were through the roof, but the women were suffering from such extraordinary osteoporosis, their hips and pelvises were shattering during childbirth.
Now if birth complications like that become commonplace in your society, you've just had it. You can't replace your population effectively, so your country just dies. Likewise, if a majority of women in your society have developed acute mental health disorders, they cannot look after their infants and children properly so infant mortality goes through the roof etc -- and your country just dies.
And, of course, women have just not been consistently treated in that way throughout Islamic history -- otherwise, there would simply be no Muslims left. What is interesting though is that Islamic structures within particular eras have allowed certain women to become extraordinarily powerful. Kosem Sultan was probably the most politically powerful person in the world in the 17th century, and she started off as a slave.
Again, cultural practices that modern western women may view as repressive actually give Muslim women from certain cultures quite an extraordinary level of power within their context. In traditional Turkic culture, a woman's domain is "the home", the domestic sphere, whereas the man's is "public space", the civic sphere.
Now this sound very patriarchal and horrendous, until you realise that "the home" is not defined by the walls of the house. It can often be the entire neighbourhood or, indeed, everything that is not the civic sphere, and the civic sphere is ahem the local coffee shop -- and that is it. 
And because "the home" is women's space, women have the authority to chuck out their husbands without argument. So if you go to them and say "you are being repressed", they will say "how?"
So the issue really isn't simple and requires a hellova lot of unpicking.
Again, and this is a bit controversial, I am pretty convinced FGM is a fairly modern practice; in my gut, I would say it originates from, at the very earliest, the 19th century. I just cannot see that FGM has been practiced for hundreds of years; its impact on fertility, childbirth and health is just too great.