As with any work of fiction, a video game is going to contain some of the designer's values and attitudes towards society. The distinction comes in (and this is something that mainstream media has a penchant for ignoring when it suits them) when you have to identify the difference between a value that is being presented by a fictional character (and so may or may not therefore be supported by the designer, usually indicated by how the character behaves otherwise; if they show other values that are usually associated with being detrimental, usually it's a value that the designer does not share) or if it's presented by the designer themselves.
Take DNF for example, the game is presented in a tongue in cheek manner that suggests the values the Duke holds are not shared by the designer. The media simply latches onto the fact that the Duke is the protagonist and so overlooks the possibility that he might intentionally be a flawed protagonist, or even a satirical parody of a protagonist.
The point is that there is a difference between the attitudes shown by a character and the attitudes shown by the game. In Mount and Blade Warband it is the characters that treat you differently, but what the OP is suggesting is that the game treats you differently. At that stage you're getting a value that is expressed explicitly by the designer. Whether that value is sexism or realism becomes subjective and you KNOW which one the media will pick up and run with. This points towards the unrealistic balance (and it is unrealistic, there is statistical evidence to prove that men are stronger than women given equal preparation (that is to say, equal training, equal nutrition etc.)) being an acceptable break from reality. Look at the 'humans' in video games more closely. How many of them need to vacate their bowels? How many need to even eat or sleep? More breaks from reality, and most of them are accepted. Perhaps it would be better if we just stopped saying they were human? Would anyone here call a game out for lack of realism if female elves were as strong as male elves?
It is intriguing though that a number of games will feature a number of species that the player can choose from for their character that influence what stats, classes, and quests are available to them but it's rare to ever get a complaint of racism. There is one factor that could possibly explain this: balance. While choosing a certain species or race in a game may be restrictive, there is no 'best' option. It's unclear why having a character's sex play a similar part as a component in a character's 'build' is considered morally grey.
To conclude, I think that having some variance isn't a bad idea as long as the game was well balanced. For every opportunity that is closed for choosing a female character, another should be opened. For every point lost in one stat, another should be gained. Above all though there should be balance in terms of how much the other characters perceive this one trait of the player character compared to others. If every character in the game behaves no differently to a beefed up warrior as they do to a nerdy academic, why should they act differently based on the player character's sex? Finally, it is VITAL that in a game with variable path options the player is ranked by most of the characters who are portrayed as being morally sound according to their past actions first, and other traits second, and to those who don't the player should have the freedom to react how they choose. To elaborate, that does not mean the player should be free of consequence. If for example the captain of the guard in a specific city is a sexist pig, if the player killed him (in a manner that would realistically get them caught) they should be arrested and whatever else then happens, but they should still have the option to try, rather than just have the guard captain be bulletproof.
