I think in some ways, Regina held Emma up to a much higher standard. Emma is the Savior after all. Knowing that the Savior could do something that is almost akin to what Cora did strikes a nerve in Regina. Now, I agree that Regina has done some fairly terrible things and that her moral highground is insanely shaky but I think it’s a heady combo of being Henry AND the deed being similar to what Cora did to her.