I am glad you posted this response. I wanted to, but couldn't come up with a proper way to state it.<quoted text>
Bingo. This IS where we differ. There's goodness for the sake of it, or goodness done merely for personal gain. In my view that is not "good".
Since atheism is mere statement of a lack of belief for something which there is no evidence it lacks motivation to do good works "in the name of atheism". To do so would merely be to want to take credit, which appears to be the Christian motivation. So in effect the numerous non-religious charitable organisations could be described as "atheistic", as they are doing good works without a need for religious motivation.
In my opinion the mention of a dearth of atheist charitable organizations was meant as an indictment of atheist values and nothing more. Your post gets to the heart of that attack and shows how valueless it really is.