There are many vaccines, if not almost all, that only prevent disease, not infection. That does not mean they are not doing their job. Reducing mortality (deaths) and morbidity (illness) can greatly increase productivity, comfort and enjoyment of a flock. Vaccines train the immune system to recognize pathogens, and it is the immune system that does all the work to eliminate or control the infection. If the immune system is not functioning well, then the vaccine will not be as effective. This is one reason why vaccinations are not completely effective. Another is that there are organisms that set up shop inside tissues such as inside nerve cells where they are inaccessible to the immune system once they get into the body, which can lead to permanent carrier status. To develop individuals that are completely immune to some infections may take centuries, or may never happen. Diseases such as Polio, Influenza, Measles, Tetanus, etc. which have been around for centuries before vaccinations were developed still ravage unvaccinated populations. If vaccinations allow individuals to survive such infections, then there is a place for them.
I certainly agree that once birds are infected by diseases such as Mareks, they should not leave the premises.