I feel the writers did this on purpose; Sunset's arc through this movie was being able to do things on her own, without the aid of Twilight to catch her when she falls. When she was presented with the situation, Twilight being turned into the thing she had turned into awhile back, she realized something. Sunset had been here before, and was just as caught up as Twilight was; Twilight turned evil because Mrs. Cinch and the gang as Crystal Prep manipulated her with the song "Unleash the Magic". In the lyrics, Mrs. Cinch informs Twilight about how she will learn about the magic her tool possess once she releases it; and there will be no other way to learn about it unless she does so. Twilight's intentions changed as she was walking to the center of the arena where the last Friendship game WOULD have commenced; from a learning opportunity to one of cheating using magic to win. I like to believe the magic in the tool around Twilight's neck can sense when a person has bad intentions rolling around inside of them, which would explain why Sunset used Twilight's crown that was for good for evil, and why Twilight became evil once she unleashed all of the magic inside of the medallion around her neck. Sunset became her counterpart because while everyone else scattered and ran away from midnight Sparkle, Sunset approached her, and tossed the medallion sprinkling the last bit of magic upon herself, obviously she had good intentions with Midnight Sparkle, the magic felt this, and she became Sunset-alicorn-person-lady.
SciTwi's motives through the whole movie was to learn all she could about magic, so of course when she became evil her motives would be to learn everything about magic...evilly.
The ending was more for Sunset's arc' realizing she had greatness in her and all that. That is why the whole segment looked like it did in EQG 1; it was done on purpose.
Wait you wanted Twilight to kill everyone?
Wat? xD