Yes, Rappaccini is a good botanist. He has a flourishing garden that attests to the devotion he has for his craft and his science. Professor Pietro Baglioni even admits to Giovanni that Rappaccini's knowledge and abilities are second to none.
"The truth is, our worshipful Doctor Rappaccini has as much science as any member of the faculty. . ."
Baglioni continues to describe some of the successes that Rappaccini has had as a botanist. The reader, and Giovanni, learn that Rappaccini has been able to modify plants and their poisons to be more deadly than anything else that nature has ever created. That statement is a clear testament to the fact that Rappaccini is essentially creating genetically modified plants. Yes, he's a good botanist.
However, Rappaccini is not a moral botanist. His goals are always to use plants to make poisons instead of cures. He feels that any discovered cures are actually failures. On top of that, Rappaccini cares very little for people. Baglioni tells Giovanni as much too.
". . . he cares infinitely more for science than for mankind."
Scientists that care more for the science are guilty of asking the question "can it be done?" and never asking the question "should it be done?" Rappaccini clearly experiments on his garden, which is one thing, but he has also clearly been experimenting on his own daughter. That's an entirely different thing. There is no doubt that turning Beatrice into a walking, talking poison is amazing science. But it is morally reprehensible science.