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Contraindications to vaccination
Almost all people should be vaccinated to stop the spread of certain preventable diseases. However, there are some people, who for medical reasons, should not receive certain vaccinations. The most common reason why a person should not receive a vaccination is if they had a severe allergic reaction to a previous vaccination (same type of vaccine) or component to a vaccine. Some people suffer anaphylactic reactions to vaccines and should not receive another vaccination of the same type of vaccine. However, these severe reactions are very rare. Severe reactions like anaphylaxis occur around 1 in a million doses given.
Another contraindication to vaccination is severe immunodeficiency. People who suffer from severe immunodeficiency have a weak immune system that is easily susceptible to infection. Some vaccinations use live, but weakened viruses. Some of these vaccinations that use a live virus include MMR, varicella, and rotavirus. These vaccines use a virus that is still able to replicate within the person receiving the vaccine. A person with severe immunodeficiency has an immune system that cannot easily fight off the weakened virus. In this case the risks outweigh the benefits for vaccination.
For a list of common vaccinations and their contraindications and precautions visit http://www.cdc.gov/vaccines/hcp/admin/contraindications-adults.html
You mentioned something that I think is important in medicine: the balance of risk and benefits. While in most cases, vaccination is recommended, in immunodeficient patients the possibility of severe reactions is much higher. Because of their compromised state, the vaccine may actually end up triggering the infection. One of my sources mentioned the importance of making sure that others around the compromised individual are up to date on their vaccines, which is something that I think is easy to overlook.
I agree that most individuals should be vaccinated and that some disorders with a SCID phenotype can prove fatal due to vaccinations. However, the majority of the population like you said, should be vaccinated and making sure the general population becomes better informed is critical. As future physicians we must strive to provide unbiased evidence and research that can allow our patients to make informed decisions. I believe presenting both sides of an issue such as this is a good idea as long as we strive to prevent harm and do good for our future patients.