There are a very small number of vaccines that would even be considered for such a program. About a dozen common ones and add maybe another dozen of epidemic or regional concerns. Vaccine manufacture is subject to high levels of scrutiny everywhere. There is nothing nefarious that can be done with a tdap or MMR vaccine when delivered via a comprehensive standardized programme. All examples I know of where bad actors used the cover of vaccines to do something else that was bad were outside those contexts. Having a known, published schedule that everyone adheres to rather than an alacarte pick n choose, is actually protective. Not as you are imagining, the perfect place to hide in plain sight. Having mass vaccine distribution and administration campaigns where everyone gets vaccines from the same source creates substantial logistical issues in doing whatever targeted mischief it is you are imagining could take place via the small number of injections over the course of a person’s life.

Your argument is like saying that because police have used excuse of traffic enforcement to wreak violence on people they don’t like, it ought not to be mandatory to build motor vehicles with seat belts.