In Jeanne d'Arc, one of your allies is Gilles de Rais. In real life, he brutally murdered and raped children, possibly in sacrifice to a demon. But in the game, he's a good guy through and through. But when you consider that at the end of the game, he allows himself to be possessed by Big Bad Gilvaroth. Who's to say that he didn't end up as such a monster after the game ended? —Master Hand
Consider some What If? factor ends here. Gilles de Rais being a child murderer may have been influenced with the lack of Joan on his side. With Joan actually still alive at the end, Gilles may be able to muster enough strength to keep Gilvaroth at bay and not turn out to be the child rapist/murderer he became in real life.
A few of the Reapers, named for some of the Seven Deadly Sins, have various complications - story-wise, or baiting the player - based on the sins.
With Superbia (Pride), Jeanne ends up locked in a room with him while the others have to fight around the map to get to her, because her overconfidence made her lower her guard and underestimate her foe.
With Avaritia (Greed), attempting to secure all the treasures on the mission can screw the player over as more monsters are periodically unleashed, culminating in a hideously over-powered dragon if you take too long.
With Ira (Wrath), you are literally fighting the wrath and anger of Roger, over Liane's death when she was mistaken for Jeanne.
In real life, Jeanne d'Arc was burned at the stake for thoughts of Witchcraft. Magic is regularly used by the player characters in-game... however, the famous Burn the Witch! still happens. It actually makes sense - Magic may be used by the characters, but they have an idea of what "Good" magic is and what "Evil" magic is. A "Witch" can be a character who got their magic power from a demon. Erego, black magic. They also sidstep this by calling Liane an "apostate".