It is unclear whether or not Baglioni knows that his antidote would kill Beatrice. On the one hand, when he sees her die after drinking it, he calls out "with horror," asking Dr. Rappaccini if his daughter's demise is the final outcome of his experiment. The fact that his voice contains anything like horror makes it sound as though the outcome was not exactly what he expected. Further, the narrator tells us that in the professional antagonism between Baglioni and Rappaccini, Rappaccini is the man believed to have the upper hand; in other words, Rappaccini may be the better scientist. Therefore, Baglioni simply might not be as smart as Rappaccini, and so the potion he prepared to be an antidote is simply incorrect.

On the other hand, when Baglioni calls out, his tone connotes "triumph" as well. If Baglioni is trying to make Rappaccini pay for besting him professionally, he might be inclined to resort to more personal means of revenge. If he is simply petty and vindictive, then it seems entirely plausible that he only wants to beat Rappaccini and he doesn't care how. In this case, then, he means to kill Beatrice as payback and to ruin the better scientist's most important experiment.