We live in a different age than most of our characters. Judging or condemning someone because of their gender, their sexual orientation, their religion, or their color is wrong in our time.
Our characters lived in a different time. Don't judge them for that and do not force them to think the way we do.
13th Century women or even most 19th century women were not feminists. They were not allowed to do what we do; they did not expect to be able to; they did not have to power to do so. Young women did not defy their parents to chose their own spouse. That doesn't mean they weren't strong people. They were as often strong as modern women, and they often did brave things--within the context of their own time. Agnes of Dunbar held her husband's castle of Dunbar against a huge English army--but she did not inherit her father's estate or title and did not expect to.
We have to allow these women to live within the standards of their own time, and if we force them to act like modern women we lose what they were.
Medieval Europeans with very, very few exceptions were Catholic. If you're not, that's fine. But your characters were if you write about that time, and you have to respect that. When one of my characters witnessed horrific acts, it was suggested that I have him question the existence of God. But this is how a modern person might react, not a medieval one.
They were not accepting of people who were Jewish or Islamic. (The people who were Islamic weren't accepting of Christians either, to avoid demonizing one side or the other) Why pretend it was otherwise? Showing the age as it was does not mean we share those beliefs. You have to be able to see the story from your character's perspective, even if you sometimes don't like that perspective.
They didn't always show mercy in war. Sometimes prisoners were executed. If you try to gloss over this, it doesn't add to the story. It takes away from it.
We should be brave enough to write them as they were rather than as they would be today. It spoils the verisimilitude of our novels and makes them anachronistic. In fact, it may date your book. Novels that did that in the 19th century now look dated. They wouldn't if the author had presented the characters and the period as they really were.
My own novel, Freedom's Sword, is based on the life of a true character, Scotland's Andrew de Moray. You can find the it at Amazon, Barnes & Noble and Smashwords.