According to Fritjof Capra in his book: The Turning Point, modern medicine and pharmacy suffer from Cartesian dualism.
But i think the problem goes back in time to ancient Greek. For example, etymologically the word "pharmakos" means a human sacrificed to the gods. And "pharmakon" has ambivalent and paradoxical meaning of both remedy and poison (see http://flutuante.wordpress.com/2009/08/01/pharmakon-the-cure-or-the-poison/). And it seems this mythology has legacy too to the present time. For instance, drugs like cocaine can be used for anesthese purpose, but in larger dose it can be lethal. Vaccination was often made of bacteria, which sometimes it can be lethal for infants (although such incidents were often neglected statistically). And sting of bees has been found to have healing effect for some types of illness, while it can also be harmful.
Another paradoxical example of modern medicine is overall low contribution of chemotherapy to cancer survival. According to a report, chemotherapy makes a minor contribution to cancer survival (around 2.3% in Australia and 2.1% in USA), although the situation also depends on the type of cancer in question (see http://weeksmd.com/2009/01/success-rate-of-chemotherapy-21-hunh/). This seems to indicate that there is much room for improvement with cancer treatment.
Furthermore, the language of warfare and battle are often used in medicine world, such as "attack" the HIV causes, "eradicate" polio etc. Such languages indicate that human illness are viewed as enemies. At the other side, in Eastern medicine, various illnesses are viewed as imbalance of the body. A healthy human body is a result if all organs function in harmony. Therefore, the purpose of medicine is to return that harmony instead of attacking the illnesses.
So, is there a chance that in the future there will be cure and medicine which are less paradoxical, just as in term of pharmakon? Your comments are welcome.