I have received some feedback that I should supply evidence for claims I have made. Since I cannot tell which part of my answer might not be commonly known or understood by others, and this topic is already taboo enough (I don't want to go linking to all sorts of hate terms that exist and hate groups or hate speeches, etc.) I ask that you please let me know what sections might need additional explanation or evidences.
This question seems to imply that sexism is something that humans that share a gender with their religious icon have toward the opposite gender, but that does not seem to be the case in reality.
The answer to your question is "yes," and it's pretty straightforward...
At least in the United States, and I'm guessing in many other areas, the generic phrase "Men are [insert negative adjective here]" is a very common phrase heard from women. In fact, sometimes it even takes the form "All men are..." One common situation where this recurs is when a woman breaks off of a romantic relationship with a man who has just offended her, and either that woman or some other woman consoling her uses that template line. I have heard it said by women even in the presence of myself and other men. It is common enough that it even appears in mainstream media.
Currently there is sexism toward men in a society where the main religion(s) are based on male messiah. Since you want to do a gender swap, just take my previous sentence and swap the genders around:
Currently there is sexism toward
men women in a society where
the main religion(s) are based on male female messiah.
If there is sexism toward men currently (and there is), then why would there not be sexism toward women if the religious icon were switched?
I will go one further...
There exists bias and bigotry against everyone for practically every aspect of their being and every type of decision they have made in their life.
Protected classes exist for a reason. The Wikipedia article on Protected Group lists some as: race, religion, national origin, age, gender, pregnancy, citizenship, familial status, disability, veteran status, and genetic information. There are also other aspects which people have, but let's concentrate on these first.
I have heard racist remarks made about every race I know of. Caucasian, African, Spanish, German, Chinese, Japanese, etc.. They all have racist hate speech made against them. I used to know a small group of guys who would frequently make awful remarks about Polish people and suffered having to hear racist remarks about them when I was around that group, and I always wondered how you could come to dislike such a random group, but the real reason is probably because hate knows no bounds.
Religion is another obvious one; we all know there is plenty of hatred and bigotry based on religion. There is a ton of it toward Muslims. Jews are another obvious religious group that receives a lot of bigoted hatred from others. I have heard plenty of it toward Christians too.
National origin is closely related to race, and I could repeat that paragraph almost verbatim.
When I was young, I was often offended by the bigotry based on age: "butt out and let the grown ups talk" or "I won't have that conversation with you until you are an adult" (this often happens even to those in their mid teens), and obviously the elderly get a lot of it as well.
Gender goes without saying. Almost everyone acknowledges the sexism against women, and most people acknowledge the comparatively less but still very real sexism toward men. If I had a dollar for every time I heard "Men are [insert negative adjective here]" I could afford to put this answer on a billboard.
Wow, I'm not even halfway through that list of protected classes and this is getting long, even though that list is not even an exhaustive list of ways people can be bigoted.
The point is that for almost every distinguishing quality or aspect a person can have, for almost every different value that quality can be, there are groups of people who hate it.
I'll add some more things people often hate over: sexual orientation, abortion, gun rights, government taxation decisions, and the list goes on.
Personally, I am Caucasian, so there are millions of people who will hate me for that on first sight, ditto for being male. Millions more would hate me for being Christian, ditto for hating abortion (as I hold the right to be alive in very high regard), and again for supporting gun rights (again, for holding right to be alive in very high regard). If everyone in the world read this answer right now, I would have millions of people who hate me when they have not even met me and have no idea what kind of person I am. Unfortunately for me, I do not hide any of this from people and so I have a lot of people who have hated me without ever getting to know me.
If there is anything you can count on when it comes to people, it is that they are very good at hating. I challenge everyone who reads this answer to think about all the different values for each thing I have listed above and to see if you don't have hate toward a general class of people over some aspect or decision. Though we commonly think of race and gender, I think you will find even more haters, likely including yourself, if you think about different options (for or against) of sexual orientation, abortion, or gun control.
The point is, yes, there will be sexism toward women in the setting you describe, because there is bigotry by almost everyone and against almost everything.