It is a historical fact that Mary Shelley came up with the story of Frankenstein during a stay with her husband Percy Bysshe Shelley, Lord Byron, and other writers. Lord Byron challenged each of his guests to come up with a horror story for the sake of entertainment. In short, Shelley's primary purpose in writing Frankenstein was to entertain rather than to warn us or to teach us a lesson in morality.
However, Shelley built her story in a parallel to the myth of Prometheus. Prometheus is the Greek god who is said to have tried very hard to bring the light of day to humanity. In a paradoxical twist, the result of Prometheus's sacrifice is to get humans expelled from heaven. Why? Because Prometheus committed an act of treason: He tampered with orders higher than his own.
Similarly, Victor Frankenstein tampers with the laws of nature in search of a knowledge that consumes him. Sadly, he obtains the same results: His ambitious experiment backfires, and Victor's creature becomes his burden.
This being said, we can conclude that, although Shelley merely aims to tell a story, she also infuses her "scary tale" with a strong central theme and adds elements that are common of her time: The discovery of nature as a force of creation and destruction, the use of rationalism, the search for the individual power of man (rationalism vs. romanticism), and the use of science as a tool for social and intellectual progress.
Nevertheless, Shelley does not seem to condemn nor condone Victor. After all, he is simply a man who pays for his mistakes perhaps in a much harsher manner than he deserves. It is more feasible to assume that, rather than warning us from something, Shelley is exposing the reality of being human. That, no matter how great our attributes may be, we are still human. We are not perfect. We are still limited.
You will undoubtedly receive many different answers regarding your question given interpretation of an idea relies solely upon an individual's ideals and thoughts regarding a work.
That being said, here are my thoughts.
I do not necessarily believe that Shelly, in the novel Frankenstein, was warning against science or medicine. Instead, I believe that she was warning against the manipulation of nature.
Man was not created to create life; yes, he is a part in the process, but the actual giving of a life belongs to woman. In nature, is is the "job" of the woman, or female of the species, to birth the next generation. God, if you are a believer in Christian thought, created woman so as to sustain mankind. If you do not follow Christian thought, you cannot deny woman's historical and scientific place as the one responsible for giving birth (besides the seahorse).
This being said, Shelly's novel places Victor as the new "Eve". He is the one who creates a new life- as a man. Another way that one could look at Victor's mirror of Eve is through her sin- she was the one who took the apple from the tree and, therefore, allowed sin to enter the world.
Shelly, for me, seems to be speaking more against the taking away of God-given rights. Victor takes away the ability for woman to be the only one to create life and, therefore, his actions become sacrilegious.