When Giovanni first speaks with his father's old friend, Professor Baglioni, the professor tells him that Dr. Rappaccini cares a great deal more about science than he does about people and that he only sees individuals as potential subjects of his experiments. However, the narrator implies that Baglioni has an axe to grind because Rappaccini and Baglioni are at odds professionally and that Rappaccini "was generally thought to have gained the advantage" in their disagreements. Therefore, it should not be terribly surprising when Baglioni continues to try to arouse Giovanni's suspicions of Rappaccini and his daughter's motives. In the end, he gives Giovanni an antidote that should reverse Beatrice's poisonous nature, and, when it kills her, he calls out triumphantly to rub the death of this experiment in his rival's face. Thus, it appears that he has manipulated Giovanni so that he could use the youth to ruin Rappaccini's most precious experiment: his daughter.
However, Rappaccini has also manipulated Beatrice and Giovanni in order to see if he could convert and procure a husband for his poisonous daughter. He seems to have purposely cultivated her poison from her birth for the sake of science, and now he wishes to take the experiment to the next level. He wants to see if he can transform a healthy youth into a poisonous one to be a mate for her daughter in this corrupted Eden. He doesn't ask his daughter what she wants, and he certainly doesn't consult Giovanni before his conversion. Beatrice ends up so miserable that she actually embraces death because "the evil" that her father has "striven to mingle with [her] being, will pass away like a dream." It doesn't seem to be her happiness that her father has sought but rather a continuation of his experiments.