The problem with the vaccination for rabies was that once an animal had been vaccinated it became impossible to distinguish (under the microscope - brain cells or neural fluids or whatever it is they have to look at for rabies detection) between an animal that had the disease and an animal that had been vaccinated, so disease control became a major issue.
I don't know if a similar thing applies with bluetongue, but I suspect there is some similarity because all the false alarms we had with imported animals turned out to be false positives from vaccinated animals. So I always assumed that was why we had to declare ourselves not disease free in order to be allowed to vaccinate; if you were actually disease-free but vaccinated, then it would be really hard to tell if the disease had really arrived.
Sorry I haven't expressed that very well - it's late and my grammer is not so good this time o' night...