Chrysalis is hungry, and so is her brood. Even after sacrificing half her forces to the other, they would not be able to hold out in their current home any longer. It was time to move. There were two things that Chrysalis wanted from her new hive once they moved in. First, they had to have a good source of food nearby. And second, to get revenge on Twilight Sparkle. Why Twilight? Because she was the one who realised she was fake of course.
Even if it means pretending to be an idiotic pony, her brood must be fed first. Her children must not be left to starve. Revenge can come later.
But it will come.