I haven't investigated Kaliah's story, so I won't comment there.
However, the 'whooping cough outbreak' story simply says that the vaccine's effectiveness decreases over time. "The majority of cases were in fully vaccinated children" - because the majority of children were fully vaccinated. The proportions given for pertussis cases line up almost exactly with the vaccination rates reported in the recent CDC survey, which certainly doesn't indicate that the vaccine makes children more susceptible.
In fact, in the linked article, the doctor running that study says that the vaccine is about 50% effective across all children, and 24% effective in the 8-12 year old age group, as effectiveness decreases; the incidence rate dips again at age 13, as that's when the booster shot occurs (which would seem to indicate that the vaccine works).
"For pertussis, having even 24 percent helps (mitigate an epidemic), but you'd sure like it higher than that," he adds.
On whether vaccination is effective, I'll add this chart: http://www.ncbi.nlm.nih.gov/pmc/article ... figure/F1/
From this 2010 study on the prevalence of disease among vaccinated and unvaccinated children (they also studied whether vaccination promoted the development of allergies and reached the conclusion that it doesn't): http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3057555/