It is not nit picking,
If you are going to blame Atheism, then you have to show that Atheism was the cause.
All sorts of people don't believe in gods.
Atheism is not a group that atheists belong to, Atheism is not like Catholicism.
An atheist doesn't need to apologise for the actions of other atheists anymore that a red head needs to apologise for the actions of other unrelated red heads.
How ever, if you are going to voluntarily join an organisation that has committed crimes you should lower your head a bit in shame when thinking about the past of that organisation, not gloss over it and try and paint it as a force for good.
I would be apologetic for the acts committed by Stalin if I was a member of a communist party with links to him, but not simply because we both shared a view that their was no gods.
Tink saying the catholic church is a force for good, would be like me saying communism is a force for good.
Me simply not believing a god exists, is not the same as me saying communism is a force for good, My lack of belief in a god has nothing to do with Stalins communist regime.
I know you believe in a deist style of god, So I don't put you in the same category as Tink, you don't have to lower your head in shame at the churches history as Tink does. Tink accepts a whole lot of doctrine which you do not, and tink supports an organisation which you do not. You simply having an opinion that a god exists won't lead you to do harm, unless you develop all sorts of other beliefs based on that opinion that transform that simple opinion into a religion, but at that point it becomes the religion that's the problem, not the simple belief or disbelief in a god.