Yes, gradually. An anti candida protocol is a lot to take for your body. It is no surprise we get reactions.
I believe allergies have a cause and can always be overcome (edit: in this particular spectrum, where we obtain allergies, not hereditary or racial for instance). There are different ways of overcoming allergies. In this case: one way is to try to heal the gut with anti inflammatory food and supplements. I havent really looked into them, but you could also check out things like NLP or bio resonance therapy.
However, beans might just not be good for you. Try it some other time. And be careful, candida is an opportunistic organism, it will come back if it gets the chance.