It wasn't anything that harsh. Once we hit her with the Elements of Harmony, she went back to her old self. Whatever darkness turned her evil in the first place? Totally gone.

[Also, Twilight as a general? Pffft. Well, she does have the right leadership qualities for it.]

As for Twilight, she's kinda like our leader, but mostly she's one of the best friends a pony could ask for. That, and Princess Celestia's student.