Chrysalis didn't become a Queen by making stupid mistakes, nor by failing to have a backup plan. So when a certain pesky purple pony starts to stick her nose where it doesn't belong, Chrysalis thinks up a plan sure to win her the day.
Twilight Sparkle is an extremely powerful mare filled with platonic love. Platonic love that's necessary in order to power one of the only weapons strong enough to eradicate Chrysalis' swarm. Platonic love that makes both Celestia and Luna hesitate to hurt the little mare. Platonic love that Chrysalis can both eat and twist to her whim.
This day is going to be perfect. If nothing else, Queen Chrysalis is at least going to have one very satisfying snack.