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.
You don't generally get to excuse bad behavior because you can make up a hypothetical different person doing the same bad thing in that situation.