The issue is that the vaccines were known to cause severe adverse reactions like death and brain damage in particular segments of the population who are especially at risk (likely IMHO to be the same segment of the population who are especially at risk from severe adverse complications arising from the disease itself...) and this information was deliberately withheld from medical practitioners and parents.
This is not a side issue it is the main issue, people have a right to informed consent.
I dare you to actually read the paper this article was based on http://www.ecomed.org.uk/wp-content/uploads/2011/09/3-tomlje....
The author does not argue that all vaccines are bad, in fact some of the important information revealed is that the authorities had knowledge that some vaccines are much worse than others (i.e. caused a lot more death and brain damage etc.) and deliberately did nothing about it in order to protect the reputation of vaccines generally.