Such a good question! If I’m trying to get to the “question behind the question,” I’d say that what the objector is pointing out is that it is morally inconsistent for God to judge someone based on something over which they have no control. From that, the atheist could argue that The Christian conception of God as morally consistent is nonsensical, and therefore can’t be true.
I think a good answer would be to challenge the assumptions underlying the objection. Notice that the atheist assumes that justice exists as an objective moral reality. The atheist also assumes that consistency is something we should strive for (see the moral imperative smuggled in again?). But on atheism, objective moral values simply don’t exist because if there is no God, moral values are subject to human opinion, making them, well, subjective! Thus, the atheist’s objection doesn’t even make sense unless God exists. So I would start there: justice as an objective moral concept, and consistency as a virtue only exist if God exists.
Now, it could be the case that God exists, but the Christian idea of human sinfulness isn’t coherent if God is just. I think the difficulty here lies in a misunderstanding of what it means for humans to be born in sin. Having a sinful nature jeans that we are inclined to reject God and instead seek our own way. But we also know the difference between right and wrong and good and evil. Thus, when we sin, even consistent with ur nature, we do so inconsistent with the objective morality that we know exists. In other words, if we commit sins due to our nature, we also know that it is sinful, making us culpable for the actions.
One can easily draw an analogy to other areas of life. Those who are predisposed to sexual sin or impulsive behaviors are stilled held accountable for acting in accordance with their impulses. This happens with drug addicts, people who are obsessive, those with narcissistic personality traits, or even sociopaths. We hope to treat such people, but what they do is still morally culpable. And dominos with human sinfulness.
The good news is that God in Christianity has not left us to a hopelessness. He has provided his Son to pay the penalty we are deserve. In other words, if God left us helpless , maybe one could object to his moral inconsistency. But he gave us the hope of his Son’s death and resurrection!