I had a similar moral conflict at a workplace and I dealt with it by resigning. Despite my outrage, I can't imagine occupying the office of my boss as an acceptable move. It's not illegal for my company to do business I disagree with, and if I don't like it, I leave. Simple.
Resigning under protest isn't really effective unless you are difficult to replace. Even in that scenario, you can almost certainly "protest" more effectively by speaking out and seeking targeted changes and then ultimately resigning or forcing them to fire you when they don't change. Protesting is at its core being an un-ignorable pain in the ass until a problem gets fixed. Resigning is pretty ignorable, especially if your reasons for doing so are not clear.
