I agree about 'greasy spoon' cafes, they usually allow changes.Surely that depends what the request is? Obviously if harissa is an ingredient in one of those dishes beloved by Masterchef where the ingredients are all piled together, then it's not going to be practical to leave it out. But if it's just a matter of not putting beans onto a plate, that shouldn't be hard to do. (If the electric system they use for ordering can't cope, then perhaps they could go back to pencil and paper.)
(My local cafe does bacon, sausage, egg, tomato, mushrooms, beans, tea/coffee, bread/toast/fried bread, and substitutions work just fine. And all for £4.50. They haven't heard of harissa - and I'm not sure they've heard of vegans either! )