I completely understand your perspective, and I hope I'm always strong enough to listen to my conscience and obey my morals.
One of the first interviews I was ever offered in a technical role was for Bechtel, in 2004. I was desperate to break into a career, I accepted the interview. I was in the car driving to the location, and just realized I couldn't do it. I couldn't ignore my morality to work for such a clear and direct war profiteer, that as a private company, had no oversight.
If I join a non-profit that has a humanitarian mission, I do so because I'm into the mission and feel fulfilled by that more than my comp. I can't imagine trading that in just because @sama got thirsty.
The mission is futile, the mission at this organization has been compromised and corrupted. Resign and continue your mission elsewhere.