No, you misunderstand. I don't think his approach is naive. My response was about consequences that take on a life of its own regardless of principled intentions. We have to separate the intentions vs consequences. Let me emphasize:
1) if one's moral principle is to not help the military, then one can stick with that principle
2) if one feels morally consistent by not accept funding from the military even if it causes some financial hardship or sacrifices, that's fine too
People have to do (or not do) things that keep them from losing sleep at night. If one has good intentions, then personal actions have to be consistent with that to maintain a clear conscience.
My entire comment has to do with consequences highlighted in this statement: "This was not what I wanted my life's work to support."
My point is that if the work has wide ranging applications, it _will_ support agendas you disagree with even if you don't take funding from the groups you oppose.
I was sensitive to that "life's work support" sentence because I'm working on a tool to let people anonymously match private data with others that have the same private data. The original motivation was letting people like-minded people discover each other without having public knowledge of it be used against them in denying future employment or denying health insurance.
However, one of my dilemmas was that it could also by used by the government and terrorist organizations. Even if I don't accept a check directly from the Department of Defense, it is inevitable they will (mis)-use the technology for purposes I don't agree with.
I think it's responsible for people to know that not accepting money from a group you oppose may not accomplish what you hope. If you think it's better to not know that, please explain why.