The program to which you refer [0] was a horrible idea. Whoever thought it up, whoever approved it, whoever fucked it up the way they did, all of those people should be fired, rather than resting comfortably in the public blind spot created by exaggerated classification. If a similar fuck-up had been perpetrated by a truly public agency, heads would have long since rolled. The CIA has never accomplished a similar operation and actually kept it secret, so it's clear that all this secrecy is focused on the American public rather than our so-called "enemies". So, thanks for bringing up this example!
I would like to point out that WHO vaccination programmes were touted as "CIA/Zionist" conspiracies way before the CIA actually used them.
Polio vaccination in Pakistan is utterly hindered because the "village elders" and the usual suspects spread nonsense that the vaccines were donated by Israel and it's a Zionist propaganda to turn the male population gay and sterile.
Is this meant as some sort of defense of this tawdry stupid CIA bullshit? The fact that a particular vaccination effort faced this particular challenge should have been a reason not to make the situation with respect to the health of poor children worse for no benefit whatsoever. When inbred goat enthusiasts harbor some zany prejudice, it is not CIA's mission to confirm that prejudice.
[0] http://www.npr.org/sections/thetwo-way/2014/05/20/314231260/...