It turns out that, when military forces pose as humanitarian workers distributing vaccines, eventually people figure that out and end up distrusting - or even attacking[2] - real humanitarian workers distributing vaccines.
(It doesn't help that similar rumors existed previously, about sterilization efforts being conducted under the guise of vaccination. But let's not forget that the reasons those rumors are credible is that the US has done similar things in the past, including against its own citizens [3]!)
The White House recently announced that they are ending spying through vaccination programs[4], though my belief is that it really has more to do with acknowledging that the tactic itself is no longer effective (as you point out), rather than a true admission of how deplorable the effects on public health are.
[0] http://www.nytimes.com/2012/07/10/health/cia-vaccine-ruse-in...
[1] https://en.wikipedia.org/wiki/Poliomyelitis_in_Pakistan
[2] http://www.rferl.org/content/feature/24803587.html
[3] https://en.wikipedia.org/wiki/Tuskegee_syphilis_experiment