I've volunteered at a large scale NPO for a number of years now holding exec positions at national and local boards. The one thing people don't understand about NPO is that non-profit doesn't mean no profit. The real difference is where the income comes from, where it goes, and how it's taxed. That's more or less it. The lash out from those who do not understand this point when you're trying to create a successful business without having to exploit sweat equity is completely frustrating.
I think GiveWell could accelerate their plans the best if they would try to make your point extremely well heard. Someone must have done a really brilliant marketing campaign somewhere along the line to convince everyone of that ideal philanthropic image of a NPO.