You pose the exact example that I use to explain my stance to separate myself from the watchtower society. Many times in the Bible the ones who were "just following orders" so to speak were punished for following someone that they presumed was gods chosen representative, when that person or entity was violating gods commands. It happened with many bad kings and it happened in the first century when loyal Jews were killed when Rome destroyed Jerusalem.
Personally, I don't believe that the watchtower society was ever "gods organization" but explaining it this way seems to make it more palatable to active jws. I think there's plenty of examples in the Bible that demonstrate that each one is responsible before god not only for their own actions, but also for their allegiances. It would be wise, therefore, to examine the organization to determine if it really is the standard of moral purity that one would expect (and indeed that it claims to be) from gods chosen representatives.