Everyone wants to believe their own delusions. Not just the religious. We all want our beliefs to be true. As you pointed out, it is how the brain works, so it is a human problem, not a religion problem.
You are correct that logic does not deconvert a theist. But then, logic generally does not change anyone's mind about anything. Think about the last time you had a political discussion where you changed someone's mind. I cannot recall when I have. Think about the last time you changed your mind about anything.
It is possible for some people to change that. But it takes training and discipline and I do not think it is possible on a broad enough scale to make much difference.
Religion is just a symptom of the inherent flaws built into our brains. Until we can fix the brain, I think we are unfortunatley stuck with religion.