Judge and his children are all capable combatants in their own right, and Judge in particular is a brilliant scientist who has worked alongside Vegapunk. It doesn't make sense to not keep them around as powerful allies to assist her in becoming pirate king and also realizing her dream of gigantifying her children and crewmates. Dumb bitch could have both Caesar AND Judge working towards realizing her ambitions and instead she's like to (try to) kill them both. The massacre just feels like a total waste of resources and combat power that does her more harm than good. I thought she was more pragmatic than this.