Joan may not have personally fought or killed anyone (though she was wounded twice), but she was indeed considered a commander.
And while it is true that the middle ages were not a quest for gender equality, women's roles were NOT limited to being slaves for the patriarchy, despite what some people think. Women could, and plenty did, become powerful in their own rights even with the deck stacked against them. It could depend on the views of the family they belonged to, but nonetheless they had options available.
Granted, these women generally didn't become powerful through military prowess. However, with the fairly minimalistic political system of Mount and Blade, portraying a completely realistic portrayal of women power might be beyond what it's capable of. So I think allowing them to become military commanders is a fair compromise. (That said, take a look at the abilities of Bannerlord's female nobles. Not all of them have stats for combat. Oftentimes, they are the girls who wear civie clothes on the profile screen. The ladies who ARE good fighters wear armor on the profile screen.)