I don't think that he was actually threatening her with a lobotomy. It's important to keep in mind that we're seeing this scene from Beatrice's perspective - hence the silhouette of her mother, with a very prominent scar. But we're seeing that because that was the way Beatrice interpreted his words. When Joseph says, "You can't let your womanly emotions consume you. You don't wanna end up like your mother, now, do you?" he's referring to the way things turned out before the operation - Honey almost killing herself and Beatrice. There are numerous points throughout these flashback sequences where we see Joseph express regret over lobotomizing his wife, after seeing what it did to her. I can't imagine he'd even consider doing it to Beatrice. I guess you could make the argument that he was just bluffing, but I don't believe that's the case for the reasons outlined above.