Thank you for your question. Unfortunately, there are many such questions that come from atheists since they try to disprove the existence of God by claiming the laws of God do not make sense. However, that is not a sensible way to approach theology nor to prove or disprove the existence of God. Rather, one must look at the arguments proving the existence of God (which include irrefutable intellectual arguments) and come to a conclusion. Once a person undertakes such a task, he/she will also arrive to the conclusion that the God which does exist is All Kind and Just and never does or commands towards anything without wisdom. Sometimes that wisdom is manifest to us and at other times, it is not. There is an aspect of worship and accepting the word of God without necessarily knowing the reason behind it (تعبّد). This does not mean we are blindly following, rather we have already established the existence of a Just Lord and know we are obeying His commands. Just because we do not know the reasoning behind certain rules does not mean we can negate the existence of the Creator!
In this instance, this atheist is doing exactly as described. In order to answer him, you need to take him back to the proofs of the existence of God and move forward from there. He, Insha Allah, will then come to realise that we are not asking anybody to 'believe in dragons' as he claims. It is futile to make an atheist understand the wisdom behind such rulings if they do not believe in God.
FYI, Islam does not allow a Muslim man to marry an atheist woman either.