It was not common for women to brandish swords or don armour, but neither was it common for orphaned blacksmiths to play a major role in a country’s politics using murder, no matter what fantasy has tried to tell us.
I propose that a story set in the period could definitely star a female protagonist and still be believable and perhaps even more interesting than a story starring a male one. One has to remember that most of European written history was written by men, during the period especially by clergy and noblemen, but also afterwards, and thus what accounts we have are coloured by that. But there are definitely examples of women playing a part in history despite the uphill battle of culture, not being the frail, meek beings who would go ugly if they educated themselves as 19th century authors would like us to believe. It is only the last couple of decades that historians and similar has really started exploring the true role of women through history.
What we have to remember, and that is easy to forget even if it sounds obvious, is that people were still people back then as they are now. History is not another dimension or a different planet. People had as varied and complex personalities and beliefs (if maybe not religious belief, at least not openly) as we have today, both men and women. And then as now some people, of either gender, broke away from the social norms and achieved spectacular things.
The catharism movement, which was a Catholic heresy a little earlier than when the game is set, had gender equality among their core tenets and even allowed female clergy. There are also notable female authors and nobles from the time, even then widely considered competent.
Most speaking example of all, though, considering the peasant origin of the player characters, is the relative prominence of women in revolts. The Peasant’s Revolt 1381 featured at least a few women as leaders for a band of rebels, as you can read here: http://www.bbc.co.uk/news/magazine-18373149
From there it should be easy to find more scholarly sources if you want to. And if you don’t want to click the link at all, here is a quote:
“On 14 June 1381, rebels dragged Lord Chancellor Simon of Sudbury from the Tower of London and brutally beheaded him. […] It was the leader of the group who arrested Sudbury and dragged him to the chopping block, ordering that he be beheaded. Her name was Johanna Ferrour.
In court documents she was described as “chief perpetrator and leader of rebellious evildoers from Kent”. She also ordered the death of the treasurer, Robert Hales. As well as leading the rebels into London, she was charged with burning the Savoy Palace - the grandest townhouse in London at the time - and stealing a chest of gold from a duke.”
That sounds like game protagonist material to me. So to conclude my long rant, I end pretty much where I started; a protagonist isn’t common. Even in a realistically, historically anchored story such as this, a female protagonist is in no way, shape or form an impossibility.
