The factors are not the same in the two comparisons.
It's people who develop these vaccines. These people have friends and family, with children. These children will be vaccinated. Why would they want to place these children at too high of a risk?
If your thesis is true, then you would expect that the children or grandchildren of pharmaceutical researchers are less likely to be inoculated. Do you think that's the case? Do you have any evidence for that?
(Personal anecdote: I once met a woman who worked at Glaxo-Wellcome, back before they became GSK. Once the chicken pox vaccine was available, she immediately got her daughter inoculated.)
There are many public health organizations besides the CDC. There's the WHO, and the public health organizations of different countries. The EU, for example, also has a very extensive set of requirements and oversight. So you can also look towards the UK, or Australia, to see what they think. (I picked English speaking countries to make it easier on you.)
There are significant differences between the CDC and NSA: 1) the NSA is institutionally secretive, while public health research is not, 2) the NSA staff are less likely to have an adverse effect by the NSA accessing their private data than the public at large, and 3) other espionage organizations, who are in the position of finding out what the NSA does, are also secretive and not likely to publish that information to the public.
I assume you considered these differences as part of your critical analysis. Why did you think they aren't significant?
* Do you have information that is not available to the CDC?
* Do you have evidence that the CDC is biased in a fashion that prevents it from being suitably "critical"?