I think you are correctly pointing out an error of logic that many atheists use. It's similar to appealing to the problem of evil as a proof against God in that appealing to it is admitting there is some objective moral standard, which requires God's existence.

Logical fallacies are to be expected if you think your thinking is just the product of random chemical reactions occurring in your brain as a response to biological needs. If that's true, nothing the human mind comes up with can really be trusted, so I guess you can believe whatever you want and it doesn't have to be logically consistent.